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<property name="body"><![CDATA[h2. About Jar Signing

If you intend to distribute an application using Java Web Start you will need to digitally sign the jar using a certificate that verifies the jars origin. MBARI provides a security certificate from [Verisign|http://www.verisign.com/] that you can use for signing your Java applications.

h3. Keystore Details

||Parameter||value||
|Keystore Location|[http://seaspray.shore.mbari.org/keystore/keystore.bin]|
|Keystore Alias|MBARIjava|
|Keystore Password|java1700|
|Key Password|javaBeansMakeLousyCoffee|

h3. Ant Example

Here's an example of how to sign your jars using [Ant|http://ant.apache.org/]

{code:xml}
<target name="sign" description="Sign jar files" >
    <property name="lib" value="lib" />
    <property name="keystore.alias" value="MBARIjava" />
    <property name="keystore.passwd" value="java1700" />
    <property name="key.password" value="javaBeansMakeLousyCoffee" />
    <property name="keystore" value="http://seaspray.shore.mbari.org/keystore/keystore.bin" />
    <signjar alias="${keystore.alias}" storepass="${keystore.passwd}" keystore="${keystore}" keypass="${key.password}">
        <fileset dir="${lib}">
            <include name="**/*.jar" />
        </fileset>
    </signjar>
</target>
{code}]]></property>
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<property name="body"><![CDATA[\\

There are&nbsp;two recommended CVS Clients to access the MBARI CVS Respository including:&nbsp;{color:#ff0000}{*}WinCVS{*}{color} and {color:#ff0000}{*}SmartCVS{*}{color}.&nbsp;&nbsp; Both clients work for all major operating systems including Windows, Macintosh, and Linux systems.&nbsp;The key bits of information to use when setting up either client are the following:
* {color:#0000cc}Your access method needs to be set to&nbsp;{color}{color:#0000cc}{*}pserver{*}{color}{color:#0000cc}&nbsp;(SmartCVS) or{color} {color:#0000cc}{*}passwd file on server{*}{color} {color:#0000cc}(WinCVS){color}
* {color:#0000cc}User&nbsp; (Your MBARI user/e-mail&nbsp;account, e.g.,{color} {color:#0000cc}{_}salamy{_}{color}{color:#0000cc}){color}
* {color:#0000cc}Repository Server (MBARI CVS Repository is hosted on{color} {color:#0000cc}{*}{_}moonjelly.shore.mbari.org{_}{*}{color}{color:#0000cc}){color}
* {color:#0000cc}CVSROOT ({color}{color:#0000cc}{*}_/home/cvs{_}{*}{color}{color:#0000cc}){color}

Thus, the full CVSROOT path for user _salamy_ would be:&nbsp;&nbsp;&nbsp; salamy@moonjelly.shore.mbari.org:/home/cvs&nbsp;

----
\\

h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Windows-7.1.6.zip|^smartcvs-win32-setup-nojre-7_1_6.zip|SmartCVS Windows version 7.1.6] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOSX-7.1.6.tar.gz|^smartcvs-macosx-7_1_6.tar.gz|SmartCVS Macintosh Version 7.1.6] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-7.1.6.tar.gz|^smartcvs-generic-7_1_6.tar.gz|SmartSVN Linux Version 7.1.6] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}({color}{color:#0066cc}{*}NOTE:*{color}{color:#0066cc}&nbsp;Setup same for MacCVS and gCVS as well){color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS Getting-Started Tutorial|^smartcvs-tutorial.pdf] \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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<property name="body"><![CDATA[Here are some notes about the deployment of the Alfresco server at MBARI:

On November 7, 2007 Todd, Kent and Kevin had a teleconference with Joe Van De Graaff and Jared from Alfresco.  We had some questions about things and wanted to get a good feel for how Alfresco should be setup for the production environment.  Joe first talked about the current situation with Alfresco licensing and where Alfresco sits with their non-profit status.  Basically, Alfresco has changed from 50% discount to a 25% discount and they are not interested in name branding or references any more (more popular now).  There are basically two version of Alfresco: Community and Enterprise.  Community is the version we are using now and Enterprise is the only supported version.  So the bottom line is that if we want any kind of support, we have to install Enterprise and to install Enterprise, we need a support contract.  There is no way to install an unsupported Enterprise version.  We then turned the discussion to Jared to talk about the technical aspects.  I am not supremely confident that Jared has done any high visibility installations, so we may have to take a step of faith on some of his answers:

# *Do you have any general recommendations on server?* Yes, see [http://wiki.alfresco.com/wiki/Repository_Hardware].  In general it looks like their configuration pages have improved see [http://wiki.alfresco.com/wiki/Server_Configuration].
# *What database is best (knowing that we prefer SQL Server)?* He said SQL Server is one of the four main supported servers (MySQL, SQL Server, PostgreSQL, and Oracle).
# *Should the database be colocated with Alfresco install?* Should not matter unless you are going over REALLY long distances.  Even if you install in same machine as Alfresco, there is no way to do direct communication, it will still go over TCP/IP stack.
# *Why are we having problems with CIFS on Mac?* Hard to tell, but probably related to authenication.  We should use passthru (we are).  We asked about being on a LINUX box operating in a Windows Domain.  He thought that might be related and running it on a Windows box might help.
# *Does Alfresco support Kerberos authentication?* Yes.  I can verify that they have documentation and examples of Kerberos setup, but I have not tried it.  Todd was curious about this as this is where MBARI is probably going for single-sign-on authentication.
# *How do companies backup/restore Alfresco?* His feeling was that the big companies are using Alfresco's export mechanism.  This seems implausible to me as there is *huge* amount of overhead associated with exporting.  He said that you could export only the rules and backup the content through CIFS.  Again, this seems silly to me.  The view through CIFS is not the file system level view of the files.  Alfresco changes the files to manage them and then makes them look like native files when you view them through CIFS.  By backing up through CIFS, you would have to restore through the Alfresco server and I am not sure that is even really possible.  The export option seems better than that.  It sound to me like the best way to backup Alfresco is to have the file storage on a NetAppliance and coordinate database backups with the NetAppliance backups.  This would mean that if the server crashed, you could restore the filesystem and the DB to the correct state and point the new server to them.  This should work, but timing is key.  We could possibly have some Alfresco downtime when the backups occur, or just do the backups during a time when we feel like there would be little chance of changes occuring during backup.  Not really an optimal situation.
# *How does failover work?*  There are two options: cold and hot.  Hot is bascially clustering (you point both servers to the same DB and file location and the clustering keeps the local caches in synch), but then you have to pay for the CPU license for the hot backup machine.  The other option (cold) is to have an identically configured server sitting dark, bug configured exactly the same way as the production server.  This would allow you to make a DNS change and then fire up the cold server if you needed to do maintenance on the production server.  The cold option means you don't need a separate license.

So, I *think* the bottom line is that we will want to have a dedicated Alfresco server, 1 CPU (quad core would be nice and maybe buy a machine with two sockets in case we want to upgrade later).  Install Windows, point to a SQL Server instance that I.S. is maintaining, map a Tornado drive on the server and use that for the locale storage.  Have an identical server configured but sitting dark.  It will take some work, but setup a backup regime that will backup the NetAppliance share and the DB at the same time (this will need to be figured out).

Here is a diagram of what this might look like:

!Alfresco Deployment.jpg|thumbnail!

If this is where we want to go, the cheapest way might be the following:

# Purchase a less potent server to use as the cold failover (maybe $4-5K)
# Purchase Gold SLA contract with Alfresco at 25% discount ($11,250)
# Configure cold server as alfresco.mbari.org, export content from oceana.shore.mbari.org and import to cold failover.
# See if engineering (or I.S.?) has a server that is not being utilized that we could put in the DMZ and migrate the Confluence and JIRA applications to that server (call this server oceana.shore.mbari.org.
# Reconfigure oceana.shore.mbari.org in the same way the cold failover was configured.  Point to the existing DB and file stores, bring down the cold failover, make a DNS switch to point to alfresco.mbari.org.  No export/import should be necessary.

So assuming we could find a server to host Confluence and JIRA, the bottom line cost would be around $15-16K with annual support contract of around $12K.  At some later time, we would probably want to purchase a test server and license (total of about $8,000, with an additional $2,800 annual contract for the test installation).]]></property>
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<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-7.0.1.zip|^smartsvn-windows-x86-setup-nojre-7_0_1.zip|SmartSVN for Windows Version 7.0.1]&nbsp;&nbsp; {color:#ff0000}*\- NEW\!*{color}

\\
\\
\\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-Mac-7.0.1.tar|^smartsvn-macosx-7_0_1.tar.gz|SmartSVN for Macintosh Version 7.0.1]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}

\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-Linux-7.0.1.tar.gz|^smartsvn-generic-7_0_1.tar.gz|SmartSVN for Linux Version 7.0.1]&nbsp;{color:#ff0000}*\- NEW\!*{color}

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h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

{color:#ff0033}{*}NOTE:*{color} {color:#ff0033}In the rare event the administrator is on vacation or unavailable, please&nbsp;submit your CVS request to the IS Remedy page at:&nbsp;{color} [https://ishelp.shore.mbari.org/helpdesk/WebObjects/Helpdesk] {color:#ff0033}and it will be assigned by IS appropriately based on urgency level.{color}

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;CVS command Line Reference. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/.&nbsp];

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

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[Welcome to CVS\!|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

[CVS Graphical User Interface (GUI) Client Software Downloads|CLT:CVS Client Software Downloads] \- {color:#3300cc}Windows, Mac, Linux Systems{color}

[Setting up&nbsp;the WinCVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]

[Adding code to CVS Repository with WinCVS GUI|CLT:Adding code to CVS Repository with WinCVS GUI]

[Command Line Access to CVS Repository&nbsp;(i.e., no GUI)|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)] *\-* {color:#3300cc}For Linux System Users{color}

[View the CVS Repository|http://moonjelly.shore.mbari.org/cgi-bin/viewvc.cgi/]\\
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h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit their respective websites.

Contact Kevin Gomes [mailto:kgomes@mbari.org], Brian Schlining [mailto:brian@mbari.org] or Kent Headley [mailto:headley@mbari.org] with questions or permission requests for certain tools.

{tip:title=External Availability}
Please note that Confluence, JIRA, and Alfresco are all available outside the MBARI firewall and can have external collaborator accounts that are not MBARI accounts.  This was a desirable feature of these tools and allows us to externally collaborate without risking security breaches at MBARI.
{tip}

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.
----
h3. Authentication and Single Sign On With Crowd

[Crowd|http://www.atlassian.com/crowd] is an authentication tool that is developed by [Atlassian|http://www.atlassian.com] and is provided to MBARI under a community/non-profit license.  It provides an internal user database so we can create external user accounts that can then be linked to other applications such as JIRA and Confluence.  It also connects to our internal MBARI user database using LDAP so that MBARI users can have Single Sign on capability across multiple applications.

Links for Crowd at MBARI:
* [Crowd Web Application|http://oceana.mbari.org:8095/crowd]
* [Documentation of MBARI Crowd Installation|SPEPRJ:MBARI Crowd Installation]

----
h3. Content Management with [Alfresco|https://alfresco.mbari.org/alfresco]

Alfresco is a Content Management System (CMS) intended to replace the Project Library on Tornado as the repository for MBARI project documentation. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

{info:title=Accounting Creates Projects in Alfresco}
One of the main benefits of Alfresco is that it can interact with our accounting system in an automated fashion. Because of this, we have the accounting system currently creating project spaces and directory structures in Alfresco automatically.  This allows the accounting software to then export all accounting activity (PDFs of AMEX, PO's, etc.) to the Alfresco spaces automatically.
{info}

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password without using "shore\" in front) to see the project library materials. The *Projects* folder is the space that contains the content for projects at MBARI.

To create a short cut to the Projects folder (or any folder), enter that folder, then select "More Actions/View Details", then "Create Shortcut" (on the right side of the page).  This will create a shortcut that will be available in the "Shelf".  To view the shortcuts in your "Shelf", click on the down arrow next to "Navigtor" on the left hand sidebar menu, then select "Shelf" and you will see your created shortcuts.

Here are some useful links related to MBARI's installation of Alfresco:
* [Alfresco's Homepage|http://www.alfresco.com/]
* [Alfresco's Developer Home Page|http://wiki.alfresco.com/wiki/Main_Page]
* [Alfresco's Enterprise Customer Portal|https://network.alfresco.com/extranet/]
* [Deployment Information for MBARI's Alfresco Installation|Deployment Information]
* [Installation Notes]
* [SPEPRJ:alfresco.mbari.org Installation Notes]
* [SPEPRJ:alfresco-test.shore.mbari.org Installation Notes]

----
h3. WIKI Collaboration Pages ([Confluence|https://oceana.mbari.org/confluence])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

# [SPEPRJ:Confluence Installation Notes]

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts an externally accessable Maven repository at [https://oceana.mbari.org/maven2], an internal repository at [http://seaspray.shore.mbari.org:8082/archiva/repository/internal/] and a repository manager at [http://seaspray.shore.mbari.org:8082/archiva]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [SPEPRJ:Maven At MBARI] for more details.

h3. Modeling with UML (JBuilder 2008 R2)

You can download JBuilder 2008 R2 from here:

[Mac OS X|http://altd.embarcadero.com/download/jbuilder/JBuilder_2008R2/jbuilder2008r2.macosx.tar.gz]
[Linux|http://altd.embarcadero.com/download/jbuilder/JBuilder_2008R2/jbuilder2008r2.linux.tar.gz]
[Windows|http://altd.embarcadero.com/download/jbuilder/JBuilder_2008R2/jbuilder2008r2.win32.zip]

Once downloaded and installed, you need to copy the following [.slip|https://alfresco.mbari.org/alfresco/webdav/Engineering/Tools/Collaboration%20Tools/JBuilder/concurrent_48444.slip] file to the:

JBUILDER_HOME/license

directory.

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[Nice that you can add custom stencils for using your own custom elements in a model. After creating a Java Project in Eclipse, I then opened a SDE project, and created diagrams, but could not get the diagram to display.  I opened the same project in the straight Visual Paradigm for UML and it seemed to work nicely.]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool list at [http://www.softdevtools.com]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Win||LINUX||Mac||Version Tested||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
| | | | | | | | | | | | | | |
||[Altova UModel|http://www.altova.com/products/umodel/uml_tool.html]|(/)|(x)|(x)|2.2|(x)|(/)|Java,C#,VB.Net|None|(/)|(/)|Windows|The windows only thing is a big issue.|$189|
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test (see [Artisan Studio]).|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]|(/)|(/)|(/)|2.0|(x)|(/)|Java,C++|Eclipse|(/) The best by far|(/) Java,C++|(?)|After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | |Still have not gotten license issues cleared up so have not been able to test|$5500/$9625 float|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]|(/)|(/)|(/)|2.1|(/)|(/)|Java/J2EE, C#, C++, CORBA IDL, .NET, XML Schema, WSDL, Database Schema, DDL Generation|(?)|Yes for Java and C++|Yes, same list as Languages|(?)|I got it up and running.  It does not generate all the clean of HTML and I could not get the roundtrip engineering to work very well.  The option to refresh the code set was greyed out so I could not synch up the code.  After laboring through it, I think I had it setup to do the code round-trip, but when I ran it, most of the classes in my diagrams disappeared and all the buttons and windows in the different panes disappeared (this could just be a Mac thing, but ouch!).  I also could not find an easy way to define associations and have them link to getter methods in the code.|This is a bit involved.  I figured we would want Enterprise mobile licenses as this allows on user to have it on three machines.  Todd Anderson bought two licenses in 1999, so we could upgrade them for $1906 (that is for both).  New mobile licenses are $1799 for locked and $2540 for concurrent.  We will most likely get academic pricing which takes of %40 so that would end up as $1079 each for locked and $1524 floating.  Maintence for new would also tack on $300 for each license. SysML and DODAF plugins cost extra and would be about $549 for both (each license).|
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[SmartDraw|http://www.smartdraw.com/exp/srd]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]|(/)|(/)|(x)|2.1|Yes, with MDG|(/)|C++, Java, C#, VB.Net, Visual Basic, Delphi, PHP, Python and ActionScript|Visual Studio and Eclipse|Yes, but I don't think automatically|Y|(?)|There are two pieces, Enterprise Architect(EA) and MDG Technology for SysML.  EA covers UML and MDG adds in SysML support. This one along with Borland one the Jolt award for 2006 for productivity. The EA tools did not really handle code well. Associations with multiplicity did not generate code correctly.|EA=$239,MDG=$100|
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue! Yep, I confirmed it.  You can tell the code generator what kind of collection you wish to use in the UML tool, but in SDE you cannot specify, it always uses object arrays (ouch!). So much for VP.|$1750 (no maint.)|
]]></property>
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<property name="body"><![CDATA[My initial impression of the product is pretty poor.  The installation was not very professional at all.  The install requirements were very picky and if you had a PATH environment variable longer than 1000 characters (most people probably do), the installation would crash.  Getting a license was very slow and their support seems like a pretty small, rag-tag bunch.

OK, got it installed and I am trying to create a new model.  You would think that would be easy.  I opened up Artisan Studio and selected File->New Model ... and then tried to create a model but kept getting "File already exists" no matter what I did.  I then looked at their online help and it says to create a new model, I have to go the the "Model Repository" and select "New Model" ... but there are no "Repositories" in the repository neighborhood.  OK, so I created an new repository on my computer.  Tried to connect to the new repository, but it is telling me it is not started.  Went to the admin tool again and started it.  Now connecting it tells me that the repository is not initialized!!!! Wow, what a user friendly tool.  OK, I have been beating on this thing, but it keeps telling me it is not initialized, but I can't find a way to initialize it.  I give up.]]></property>
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<property name="versionComment"><![CDATA[added link to the OGC Oceans IE entry]]></property>
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<property name="body"><![CDATA[Phone conversation with support guys.  I have been working with Ahmad 1 (800) 656-3035 (option 1, then extension 7917).

Eric, Ahmad:

.NET: Microsoft has done their own visual modeling, IBM will not compete.  Software architect does not support .NET, 3rd party can reverse .NET.  Pretty loose coupling. Software architect, fairly close to Together (code visualization), harvesting (reverse), (forward) transformation: java, c++.  ORM - Lightweight: visualization of databases - EJBs are supported (EE 5 will be supported).  Serious data modeling (database architect, separate product). Difference with Together (very similar).  Big difference is what tools it integrates with (testing, requirements). Rational Rose Technical Developer is the place to go for embedded systems.  Moving into RSA (probably 2 years).

Dan Thompson: (Boulder, CO) is my regional sales rep.

Ahmad came back with quotes:

Gov't qualification: drop %25.  5 user licenses ($5500/user if govt $4637) or 2 floating ($9625/license if govt. $8114/license). Preferred business partners could bring it down some.]]></property>
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<property name="body"><![CDATA[Brian was trying to build a set of classes, but could not get it to work.]]></property>
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<property name="body"><![CDATA[----
h2. Adding your code

Here's the standard method of adding a new directory to the subversion repository.

1) On your local machine create the following directory structure
{noformat}
tempdir
`~~ myproject       <-- Replace 'myproject' with the name of your project
   `~~ tags
   `~~ branches
   `~~ trunk
      `~~ agent
      `~~ ctd2007
{noformat}
2) cd to _tempdir_ and run the following command
{{svn import myproject svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject}}

3) To check out _myproject's_ main trunk on another machine you run the command
{{svn co svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject/trunk myproject}} {note:title=Be Careful}


Notice that we've added '/trunk' to the SVN URL above to check out only the trunk (main development line). If you omit '/trunk' you will check out all tags and branches as well as the trunk. {note}\\
\\

A free on-line guide to SVN is available at [http://svnbook.red-bean.com/]. The most useful svn commands are
\\
{noformat}
svn status                            <-- shows you the status of files in your project
svn add some/new/file                 <-- add a new file to version control
svn del some/old/file                 <-- remove a file from version control
svn update                            <-- Get changes from the repository
svn commit -m "some commit message"   <-- commit changes to the repository
svn help
{noformat}
If you find that you can't connect to the svn repository contact Karen Salamy (salamy@mbari.org). She may need to give you access permissions.]]></property>
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h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on *{+}Linux systems{+}* with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your account, you will need to log in to the CVS Repository.&nbsp; You should only have to do this once in the window you are using during&nbsp;each session.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}cvs login{*}{color}\\
\\
\\

You should get the following response from the computer:

*Logging in to :pserver:*{*}{_}your_userName{_}{*}*@moonjelly.shore.mbari.org:2401/home/cvs*
*CVS password:*
\\

Enter your CVS password at the prompt.&nbsp; If you have entered the correct password you will be returned to a &nbsp;*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$*&nbsp;&nbsp;prompt.&nbsp; You are now logged in and can access project modules on the system.&nbsp; If you receive a login error from the system, re-check your password as forgotten passwords&nbsp;is the number one problem experienced by CVS users.&nbsp; If the problem persists, please contact Karen Salamy (the CVS Repository Administrator):&nbsp; {color:#3300cc}salamy@mbari.org&nbsp;&nbsp;{color} {color:#000000}.{color}
\\
\\
\\

----
h3. CVS Command Line Usage

\\

\\
CVS has an *enormous* number of commands and options available. Usage of Command Lines for CVS requires familiarization with the command calls.&nbsp;&nbsp;A common link is&nbsp;provided below to help get started:

*[*CVS Command Line Reference Guide*|https://oceana.mbari.org/confluence/download/attachments/54/CVS-commandline-reference.pdf?version=1]*

\\
\\

----
h3. Additional Usage Guidance

_(from_ http://badgertronics.com/writings/cvs/command-line.html_)_

\\
The general format of CVS commands is:

% cvsgeneral-optionscommand-namecommand-specific-optionsfilename

Here's how to get help:
| cvs \--help-commands | Show all of the commands |
| cvs \--help-options | Shows the "global" options, which apply to all commands. The most useful of these is \-n, which doesn't execute anything that will change files stored on the disk, but shows what work it would have done. |
| cvs \-H command | Show the command-specific options. |

h3. Task Reference

|| Action || How to do it. ||
| Sync your tree with the repository. \\
See what files are modified or haven't been checked in | cvs update(sample) |
| See complete revision history for a file | cvs log filename(sample) |
| See revision comment for one revision | cvs log \-r1.5 filename |
| See the differences between a file and its last checked in version | cvs diff filename |
| See the differneces between two checked-in revisions of a file | cvs diff \-r1.4 \-r1.7 filename(sample) |
| See who modified each line of a file, with what revision | cvs annotate filename(sample) This is handy when you see a line of really bogus code and you want to know who was reponsible. |
| Add a new file to the repository | Create the file \\
cvs add filename \\
cvs commit \-m "Initial Revision" filename |
| Add a new binary file to the repository | Create the file \\
cvs add \-kb filename \\
cvs commit \-m "Initial Revision" filename A "binary file" won't have CVS keyword expansion performed on it. \\ |
| Add a new directory to the project | cd to the directory's parent cvs add directoryname |
| Checking a file's changes into the repository. | cvs commit \-m "check-in comment" filenameIf your check-in comment is more than one line, leave off the the \-m option and use the editor that is brought up. |
| Revert a file to its last checked-in revision | Remove the file \\
cvs update filename |
| Add a whole directory tree as a new project | cdto the project directory \\
cvs import \-m "project name" directory "ArsDigita" "initial-development" Note that this does not change directory into a CVS-controlled tree. You'll need to remove the tree and check it out. |
| Check out a whole project | cvs checkout project-name |
| Label a tree for concurrent development | cd to the parent directory of your tree \\
cvs tag \-R \-b labelname This will use the currently-checked-out versions of the files as they exist in your directory tree. \\
The \-b argument means that this tag is a "branch" tag, meaning that someone can check out a new tree based on this tag and do development. \\
If you omit the \-b, the label will be a "sticky" tag, meaning that someone won't be able to check in new changes under that label. See the notes on Labeling and Branching |
| Check out a tree based on a label | cvs checkout \-r labelname projectnameIf labelname was created as a "branch" tag, then you can check in changes without affecting anyone using the development tip. Otherwise files are considered "sticky" and changes cannot be checked in. |
| Change a file to be treated as a binary file after it's been added | cvs admin \-kb filename A "binary file" won't have CVS keyword expansion performed on it. |

h3. \\

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----
h2. Standard method of operation for working with the CVS GUI clients


h6.

{color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator (_Karen Salamy:&nbsp;_ salamy@mbari.org). Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see:_ [Seeting up a CVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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h5. Desired behavior
# We can create accounts on Subversion (Crowd local store is where we can do this) for external collaborators.  This will prevent them from having any access to MBARI resources.
# It may eventually get to the point where users can create new repositories (projects), but for now, we will assume that the process of creating a new project is a manual one done by an admin.
# There is one repository per project.

h5. References
# [Integrating Crowd with Apache|http://confluence.atlassian.com/display/CROWD/Integrating+Crowd+with+Apache]
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<property name="body"><![CDATA[----
h3. *{+}Welcome to CVS\!+*

CVS is the MBARI Software Engineering source code repository which resides on the Linux server '{color:#3300ff}{_}moonjelly{_}{color}'.&nbsp;&nbsp;Someone has&nbsp;requested that you be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

h3. \\


h3. +Permissions+

Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout the project for security purposes.&nbsp;
\\
&nbsp;

h3. +Password Access+

Access to the repository requires another (_separate_) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network (_usually with the command prompt, Cygwin Window, or a Linux Terminal_) by logging in to moonjelly via {color:#3300ff}{*}ssh{*}{color} with your standard MBARI password (example: ssh salamy@moonjelly.shore.mbari.org).  This will run the script: &nbsp;{color:red}{*}encryptCVSpw{*}{color}

Follow the onscreen instructions to create an encrypted version of your password.&nbsp; You may put any password in that you wish - even the same one as your standard MBARI network password.&nbsp; That is up to you.  The system will then email you a copy of your encrypted password.  *{+}Please forward that e-mail to me+* so that I may add/update your password to the repository password list.&nbsp; I will then send you an e-mail when you are able to access the repository.

NOTE:_moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot access _moonjelly_ for any reason, please let me know.
\\
&nbsp;

h3. *{+}CVS GUIs{+}*

GUIs are the main way users interact with the repository to checkout, edit, and checkin files. I highly recommend the "Free" [SmartCVS Client|http://www.syntevo.com/smartcvs/download|Download SmartCVS Client] version to access moonjelly.  However, there are many other free clients including WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) should you prefer them. You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the link [Setting up WinCVS_1.2|^Setting_up_WinCVS_1.2_new.doc]. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. Please&nbsp;remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

Regards, - Karen A. Salamy (_MBARI CVS administrator)_ \- salamy@mbari.org
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# ADCP: Acoustic Doppler Current Profiler - a sonar that attempts to produce a record of water current velocities for a range of depths [http://en.wikipedia.org/wiki/Acoustic_Doppler_Current_Profiler]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AMQP: Advanced Message Queuing Protocol - [http://www.amqp.org]
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ARI-WG: Access to Remote Instrumentation in a distributed environment - Working Group. OpenGrid Forum [http://www.ogf.org/gf/group_info/view.php?group=ari-wg]
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CGSN: Coastal & Global Scale Nodes - [http://www.whoi.edu/ooi_cgsn/home]
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EarthCube: EarthCube is a NSF activity to create a data and knowledge management system for the 21st Century. The scientific objective is to develop a framework over the next decade to understand and predict the Earth system from the sun to the center of the Earth [http://earthcube.ning.com/]
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GNB: Gaussian Naïve Bayes. GNB is a probabilistic classifier relying on Bayes rule to estimate posterior probabilities of labels given the data. Naive assumption in it is an independence of the features. See [http://en.wikipedia.org/wiki/Naive_bayes] for more information.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GRIIDC: Gulf of Mexico Research Initiative Information and Data Cooperative [https://data.gulfresearchinitiative.org/about]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# HDF: Hierarchical Data Format
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# JVM: Java Virtual Machine - [http://en.wikipedia.org/wiki/Jvm]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LCM: Lightweight Communications and Marshalling [https://lcm-proj.github.io/]
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MB/CA Current: a MBARI project in 2011
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MODIS: Moderate Resolution Imaging Spectroradiometer is a key instrument aboard the Terra (EOS AM) and Aqua (EOS PM) satellites.
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# MVC: Model-View-Controller software pattern - [http://en.wikipedia.org/wiki/Model%E2%80%93view%E2%80%93controller]
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NODC: National Oceanographic Data Center - [http://www.nodc.noaa.gov/]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTP: Network Time Protocol - a protocol to synchronize the clocks of computers over a network. [http://www.ntp.org/]
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# ODSS: Oceanographic Decision Support System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOI CI: Ocean Observatories Initiative CyberInfrastructure: [http://ci.oceanobservatories.org/] (Developers site: [http://ooici.net/])
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/];  Also Robot Operating System [http://www.ros.org/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software).
# SCPI: Self Contained Plankton Imager, an MBARI project in 2011
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TRN: Terrain-Relative Navigation. Using sensors that can "read" nearby terrain and comparing that with a known map of the area to determine where you are.
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WCS: Web Coverage Service
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

{note:title=Test Machine Installation Difference}
I also setup a test machine to help Alan Lash have something to develop against and for me to test somethings like using MS SQL Server instead of my SQL.  I will write notes where the instructions differ.  I setup the test machine on ssdsdevpc.shore.mbari.org which is an HP desktop machine running Fedora Core 7.
{note}

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 (tomcat version) from alfresco.org (the tar.gz file and moved it to /opt)
{note:title=Test Machine Installation Difference}
On the test machine, I installed Alfresco 2.1 tomcat version
{note}
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
{note:title=Test Machine Installation Difference}
I.S. was hoping to get Alfresco to run against the institutes MS SQL Server for support reasons so on the test machine, I used a database named 'Alfresco' on our database server solstice.shore.mbari.org.  Neil created the database for me and the user DB_Collaboration was used to access it.
{note}
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
{note:title=Test Machine Installation Difference}
Fedora core 7 had 5.2.2 installed
{note}
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
{note:title=Test Machine Installation Difference}
I named the directory alfresco-2.1
{note}
# I then moved the tar into the alfresco-2.0 directory
{note:title=Test Machine Installation Difference}
alfreso-2.1 directory
{note}
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
{note:title=Test Machine Installation Difference}
This was a bit different in FC7.  In order to get Xvfb installed I used "Add/Remove Software" to install it.  OpenOffice was already installed so I just had to find the soffice command location.  The command to get Xvfb running was also a bit different.  I had to create a ascii file called /etc/xvfb-auth.cfg that only had one line in it that read 'localhost'.  Then the command to start Xvfb was 'Xvfb :1 -auth /etc/xvfb-auth.cfg'.  Then I could start soffice the same way.  I changed the start_oo.sh file to reflect those commands.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
{note:title=Test Machine Installation Difference}
Did not do this
{note}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
{note:title=Test Machine Installation Difference}
/data/alfresco-2.1
{note}
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
{note:title=Test Machine Installation Difference}
This file already existed and was no different from the sample, so I skipped this step
{note}
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
{note:title=Test Machine Installation Difference}
This file already existed and so copied the original to custom-repository.properties.orig and edited the existing one.
{note}
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
{note:title=Test Machine Installation Difference}
I changed them to work with the MS SQL Server login so they looked like:
db.username=DB_Collaboration
db.password=********
db.pool.initial=10
db.pool.max=100
{note}
### I commented out the two HSQL connection lines
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
{note:title=Test Machine Installation Difference}
Left the MySQL lines commented out, but uncommented the SQLServer lines and changed them to
db.driver=net.sourceforge.jtds.jdbc.Driver
db.url=jdbc:jtds:sqlserver://solstice.shore.mbari.org/Alfresco;domain=SHORE;user=DB_Collaboration;password=******
{note}
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
{note:title=Test Machine Installation Difference}
Already existed, so backuped up to .orig and edited to comment out the HSQL and uncomment the SQLServer one.
{note}
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
{note:title=Test Machine Installation Difference}
The downloaded alfresco already has the MySQL driver jar in the install, but since I am using SQLServer, I downloaded the jtds driver from the internet and installed the jtds-X.X.X.jar file in the /opt/alfresco-2.1/tomcat/common/lib to make it available to alfresco.
{note}
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0.  I also added the following line after the line that stated 'killall soffice.bin':
killall Xvfb.  That ensured the Xvfb process was killed when alfresco was shutdown.
{note:title=Test Machine Installation Difference}
Set it to /opt/alfresco-2.1/tomcat for the test machine
{note}
{tip}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{tip}
{note:title=Test Machine Installation Difference}
For the test machine, I wasn't too worried about details, so I skipped the next 15 or so steps (picks up again at configuring for MBARI LDAP below.
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{tip}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{tip}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{tip}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{tip}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## We wanted to be able to make sure we could have collaborator accounts that were not MBARI LDAP accounts so that we could have Alfresco users that had not permissions at all on the MBARI network.  In order to do this, I used the Alfresco native user service and chained the authentication together with the MBARI LDAP.  In order to do this, I copied the chaining-authentication-context.xml.sample to chaining-authentication-context.xml.  I then edited the file to make the appropriate changes (I have also attached the changed config file [here|^chaining-authentication-context.xml] for downloading):
### The first change was to the first bean declaration's id from *authenticationServiceImpl* to *authenticationService*.
### In the same bean declaration, I changed the first authentication services reference from *authenticationServiceImplJAAS* to *authenticationServiceImplLDAP* 
### I then changed the JAAS bean declaration to point to the ldap declaration by changing the bean id from *authenticationServiceImplJAAS* to *authenticationServiceImplLDAP*
### There are two properties in this bean and I had to change them to point to the LDAP configuration (these changes actually reference the services defined in the ldap-authentication-context.xml configuration file).
#### Change the authenticationDao property's value from *authenticationDaoJAAS* to *authenticationDaoLDAP*
#### Change the authenticationComponent property from *authenticationComponentImplJAAS* to *authenticationComponentImplLDAP*
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponent" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
{note:title=Test Machine Installation Difference}
Did not setup SSL for the test machine
{note}
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{tip}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{tip}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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</property>
</object>
<object class="Page" package="com.atlassian.confluence.pages">
<id name="id">133</id>
<property name="title"><![CDATA[UML]]></property>
<collection name="bodyContents"><element class="BodyContent" package="com.atlassian.confluence.core"><id name="id">131</id>
</element>
</collection>
<property name="version">25</property>
<property name="creatorName"><![CDATA[kgomes]]></property>
<property name="creationDate">2006-10-29 22:01:14.287</property>
<property name="lastModifierName"><![CDATA[kgomes]]></property>
<property name="lastModificationDate">2006-10-31 14:14:37.377</property>
<property name="versionComment"><![CDATA[]]></property>
<property name="originalVersion" class="Page" package="com.atlassian.confluence.pages"><id name="id">101</id>
</property>
<property name="contentStatus"><![CDATA[current]]></property>
</object>
<object class="Page" package="com.atlassian.confluence.pages">
<id name="id">9372371</id>
<property name="title"><![CDATA[MBARI Acronym Page]]></property>
<collection name="bodyContents"><element class="BodyContent" package="com.atlassian.confluence.core"><id name="id">9405103</id>
</element>
</collection>
<property name="version">3</property>
<property name="creatorName"><![CDATA[kgomes]]></property>
<property name="creationDate">2009-03-25 14:42:40.200</property>
<property name="lastModifierName"><![CDATA[kgomes]]></property>
<property name="lastModificationDate">2009-03-25 15:13:07.927</property>
<property name="versionComment"><![CDATA[]]></property>
<property name="originalVersion" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
</property>
<property name="contentStatus"><![CDATA[current]]></property>
</object>
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<id name="id">134</id>
<property name="title"><![CDATA[UML]]></property>
<collection name="bodyContents"><element class="BodyContent" package="com.atlassian.confluence.core"><id name="id">132</id>
</element>
</collection>
<property name="version">26</property>
<property name="creatorName"><![CDATA[kgomes]]></property>
<property name="creationDate">2006-10-29 22:01:14.287</property>
<property name="lastModifierName"><![CDATA[kgomes]]></property>
<property name="lastModificationDate">2006-10-31 14:15:43.217</property>
<property name="versionComment"><![CDATA[]]></property>
<property name="originalVersion" class="Page" package="com.atlassian.confluence.pages"><id name="id">101</id>
</property>
<property name="contentStatus"><![CDATA[current]]></property>
</object>
<object class="Page" package="com.atlassian.confluence.pages">
<id name="id">9372372</id>
<property name="title"><![CDATA[MBARI Acronym Page]]></property>
<collection name="bodyContents"><element class="BodyContent" package="com.atlassian.confluence.core"><id name="id">9405104</id>
</element>
</collection>
<property name="version">4</property>
<property name="creatorName"><![CDATA[kgomes]]></property>
<property name="creationDate">2009-03-25 14:42:40.200</property>
<property name="lastModifierName"><![CDATA[kgomes]]></property>
<property name="lastModificationDate">2009-03-25 15:14:20.507</property>
<property name="versionComment"><![CDATA[]]></property>
<property name="originalVersion" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
</property>
<property name="contentStatus"><![CDATA[current]]></property>
</object>
<object class="Page" package="com.atlassian.confluence.pages">
<id name="id">131</id>
<property name="title"><![CDATA[UML]]></property>
<collection name="bodyContents"><element class="BodyContent" package="com.atlassian.confluence.core"><id name="id">129</id>
</element>
</collection>
<property name="version">23</property>
<property name="creatorName"><![CDATA[kgomes]]></property>
<property name="creationDate">2006-10-29 22:01:14.287</property>
<property name="lastModifierName"><![CDATA[kgomes]]></property>
<property name="lastModificationDate">2006-10-31 09:13:30.480</property>
<property name="versionComment"><![CDATA[]]></property>
<property name="originalVersion" class="Page" package="com.atlassian.confluence.pages"><id name="id">101</id>
</property>
<property name="contentStatus"><![CDATA[current]]></property>
</object>
<object class="Page" package="com.atlassian.confluence.pages">
<id name="id">132</id>
<property name="title"><![CDATA[UML]]></property>
<collection name="bodyContents"><element class="BodyContent" package="com.atlassian.confluence.core"><id name="id">130</id>
</element>
</collection>
<property name="version">24</property>
<property name="creatorName"><![CDATA[kgomes]]></property>
<property name="creationDate">2006-10-29 22:01:14.287</property>
<property name="lastModifierName"><![CDATA[kgomes]]></property>
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h3. *Setting up WinCVS (v. 1.2) on your Windows 2000/XP (x86) computer to access the MBARI&nbsp;*{*}{_}moonjelly{_}* *CVS source code repository.*&nbsp;

*1).* To install WinCVS 1.2 on your computer please click the following link: [{color:#ff0000}{*}WinCVS-1.2.0 Download{*}{color}|^WinCvs120.zip]&nbsp;and&nbsp;download&nbsp;the *{_}WinCVS-1.2.0.zip{_}* folder to your Desktop.&nbsp; Extract all files to your *{_}C:\Program_Files{_}*&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
*2).* Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as *{_}C:\Program_Files\GNU\WinCVS_1.2{_}* .

\\
*3).*&nbsp;Once installed, open WinCVS (*{_}Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS{_}*).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says *"ENTER THE CVSROOT"* .&nbsp; An example of this would be (_salamy@moonjelly:/home/cvs_) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the *"AUTHENTIFICATION:"* setting to - *_"passwd" file on the cvs server._*
* Finally, click the _WinCVS_ tab and set your *"home"* directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).
\\

\\
*&nbsp;4).*&nbsp;*NOTE:*&nbsp; To actually use this GUI on the moonjelly repository you will first need an excrypted CVS respository password (see also&nbsp;*"Password Access"* at the following link: [https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21]
* To do this, telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command {color:#ff0000}{*}{+}encryptCVSpw{+}{*}{color}.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (\*_exactly as listed_\*) to the CVS&nbsp;administrator (*salamy@mbari.org). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.
\\
\\
\\

*5).*&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
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----
h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.&nbsp;

To use SVN first requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org). {color:#ff0033}{*}NOTE:*{color} {color:#ff0033}In the rare event the administrator is on vacation or unavailable, please&nbsp;submit your&nbsp;SVN request to the IS Remedy page at:&nbsp;{color} [https://ishelp.shore.mbari.org/helpdesk/WebObjects/Helpdesk] {color:#ff0033}and it will be assigned by IS appropriately based on urgency level.{color}

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

\\
&nbsp;

[SVN Client Software Downloads|CLT:SVN Client Software Downloads] {color:#ff0000}\- Windows, Macs, Linux Systems{color}

[Setting up SVN Client&nbsp;to MBARI SVN Repository|CLT:Setting up SmartSVN]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository] {color:#ff0000}\- Non&nbsp;SVN client&nbsp;method{color}

[View the SVN Repository|http://kahuna.shore.mbari.org/viewvc]\\
\\
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----
h3. Download and Install Client&nbsp;

To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
To set up the SmartSVN client, run the application.&nbsp; Next, choose "*Project"* from the&nbsp;Main Menu and then click on "*Check Out..."*

This should bring you to the following page:

\\ !Screen_Save_Checkout_small.jpg|align=left!\\
\\
\\

Click on the&nbsp;*"Manage"* button, create&nbsp;and edit a new profile called&nbsp;*"MBARI_SVN"*&nbsp;as follows:

\\ !Screen_Saver_Edit_Repo_small.jpg|align=left!\\
\\ {color:#ff0000}{*}NOTE\!\!&nbsp;*{color} Make sure you use your own personal *Login Name* when creating this profile and check that the *"Verify connection when pressing 'OK'"* box is clicked in order to verify that your computer is able to connect with the SVN server kahuna.
\\
\\
\\
Once you have&nbsp;properly set up your Profile Name, when you click&nbsp;*"Project"* and *"Check&nbsp;Out..."* from the&nbsp;Main Menu, you should see a&nbsp;a page to login to your account on the repository.&nbsp; Use your standard MBARI network account to log in.&nbsp; Once you have logged in successfully, you will see a list of all projects&nbsp;on&nbsp;the&nbsp;MBARI SVN&nbsp;Repository.\\

\\
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<id name="id">3277229</id>
<property name="viewCount">18</property>
<property name="url"><![CDATA[http://oceana:8081/display/CLT/Collaboration+Tools+Home+Page]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">879</id>
</property>
<property name="creatorName"/><property name="creationDate">2008-04-10 13:14:15.123</property>
<property name="lastModifierName"/><property name="lastModificationDate">2008-04-24 15:50:15.053</property>
</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133606</id>
<property name="destinationPageTitle"><![CDATA[//www.ntp.org/]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
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<property name="lastModifierName"><![CDATA[carueda]]></property>
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</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133607</id>
<property name="destinationPageTitle"><![CDATA[//www.oceansites.org/]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
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<property name="creatorName"><![CDATA[carueda]]></property>
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</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133608</id>
<property name="destinationPageTitle"><![CDATA[//www.oceansites.org/]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
</property>
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<property name="lastModifierName"><![CDATA[carueda]]></property>
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<object class="ReferralLink" package="com.atlassian.confluence.links">
<id name="id">3277232</id>
<property name="viewCount">6</property>
<property name="url"><![CDATA[http://oceana:8081/display/CLT/SVN+at+MBARI]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">54</id>
</property>
<property name="creatorName"/><property name="creationDate">2008-04-10 14:05:15.063</property>
<property name="lastModifierName"/><property name="lastModificationDate">2008-04-24 10:59:15.020</property>
</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133609</id>
<property name="destinationPageTitle"><![CDATA[//www.opengeospatial.org/]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
</property>
<property name="creatorName"><![CDATA[carueda]]></property>
<property name="creationDate">2015-01-14 16:09:56.043</property>
<property name="lastModifierName"><![CDATA[carueda]]></property>
<property name="lastModificationDate">2015-01-14 16:09:56.043</property>
</object>
<object class="ReferralLink" package="com.atlassian.confluence.links">
<id name="id">3277233</id>
<property name="viewCount">1</property>
<property name="url"><![CDATA[http://oceana:8081/pages/createpage.action?spaceKey=CLT]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">3114617</id>
</property>
<property name="creatorName"/><property name="creationDate">2008-04-10 14:07:15.020</property>
<property name="lastModifierName"/><property name="lastModificationDate">2008-04-10 14:07:15.020</property>
</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133610</id>
<property name="destinationPageTitle"><![CDATA[//www.oostethys.org/ogc-oceans-interoperability-experiment]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
</property>
<property name="creatorName"><![CDATA[carueda]]></property>
<property name="creationDate">2015-01-14 16:09:56.043</property>
<property name="lastModifierName"><![CDATA[carueda]]></property>
<property name="lastModificationDate">2015-01-14 16:09:56.043</property>
</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133611</id>
<property name="destinationPageTitle"><![CDATA[//www.ogf.org/]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
</property>
<property name="creatorName"><![CDATA[carueda]]></property>
<property name="creationDate">2015-01-14 16:09:56.043</property>
<property name="lastModifierName"><![CDATA[carueda]]></property>
<property name="lastModificationDate">2015-01-14 16:09:56.043</property>
</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133635</id>
<property name="destinationPageTitle"><![CDATA[//en.wikipedia.org/wiki/RS-232]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
</property>
<property name="creatorName"><![CDATA[carueda]]></property>
<property name="creationDate">2015-01-14 16:09:56.043</property>
<property name="lastModifierName"><![CDATA[carueda]]></property>
<property name="lastModificationDate">2015-01-14 16:09:56.043</property>
</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133634</id>
<property name="destinationPageTitle"><![CDATA[//en.wikipedia.org/wiki/Computer]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
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<property name="creatorName"><![CDATA[carueda]]></property>
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<property name="lastModifierName"><![CDATA[carueda]]></property>
<property name="lastModificationDate">2015-01-14 16:09:56.043</property>
</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133633</id>
<property name="destinationPageTitle"><![CDATA[//en.wikipedia.org/wiki/Data_circuit-terminating_equipment]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
</property>
<property name="creatorName"><![CDATA[carueda]]></property>
<property name="creationDate">2015-01-14 16:09:56.043</property>
<property name="lastModifierName"><![CDATA[carueda]]></property>
<property name="lastModificationDate">2015-01-14 16:09:56.043</property>
</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133632</id>
<property name="destinationPageTitle"><![CDATA[//en.wikipedia.org/wiki/Data_terminal_equipment]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
</property>
<property name="creatorName"><![CDATA[carueda]]></property>
<property name="creationDate">2015-01-14 16:09:56.043</property>
<property name="lastModifierName"><![CDATA[carueda]]></property>
<property name="lastModificationDate">2015-01-14 16:09:56.043</property>
</object>
<object class="ReferralLink" package="com.atlassian.confluence.links">
<id name="id">161</id>
<property name="viewCount">8</property>
<property name="url"><![CDATA[http://oceana:8081/dashboard.action?spacesSelectedTab=all]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">54</id>
</property>
<property name="creatorName"/><property name="creationDate">2006-11-20 09:08:15.027</property>
<property name="lastModifierName"/><property name="lastModificationDate">2008-04-24 12:36:15.017</property>
</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133631</id>
<property name="destinationPageTitle"><![CDATA[//en.wikipedia.org/wiki/Serial_communications]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
</property>
<property name="creatorName"><![CDATA[carueda]]></property>
<property name="creationDate">2015-01-14 16:09:56.043</property>
<property name="lastModifierName"><![CDATA[carueda]]></property>
<property name="lastModificationDate">2015-01-14 16:09:56.043</property>
</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133630</id>
<property name="destinationPageTitle"><![CDATA[//www.ros.org/]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
</property>
<property name="creatorName"><![CDATA[carueda]]></property>
<property name="creationDate">2015-01-14 16:09:56.043</property>
<property name="lastModifierName"><![CDATA[carueda]]></property>
<property name="lastModificationDate">2015-01-14 16:09:56.043</property>
</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133629</id>
<property name="destinationPageTitle"><![CDATA[//www.rosys.com/]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
</property>
<property name="creatorName"><![CDATA[carueda]]></property>
<property name="creationDate">2015-01-14 16:09:56.043</property>
<property name="lastModifierName"><![CDATA[carueda]]></property>
<property name="lastModificationDate">2015-01-14 16:09:56.043</property>
</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133628</id>
<property name="destinationPageTitle"><![CDATA[//orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
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<property name="creatorName"><![CDATA[carueda]]></property>
<property name="creationDate">2015-01-14 16:09:56.043</property>
<property name="lastModifierName"><![CDATA[carueda]]></property>
<property name="lastModificationDate">2015-01-14 16:09:56.043</property>
</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133627</id>
<property name="destinationPageTitle"><![CDATA[//en.wikipedia.org/wiki/RAID]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
</property>
<property name="creatorName"><![CDATA[carueda]]></property>
<property name="creationDate">2015-01-14 16:09:56.043</property>
<property name="lastModifierName"><![CDATA[carueda]]></property>
<property name="lastModificationDate">2015-01-14 16:09:56.043</property>
</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133626</id>
<property name="destinationPageTitle"><![CDATA[//www.mbari.org/pw]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
</property>
<property name="creatorName"><![CDATA[carueda]]></property>
<property name="creationDate">2015-01-14 16:09:56.043</property>
<property name="lastModifierName"><![CDATA[carueda]]></property>
<property name="lastModificationDate">2015-01-14 16:09:56.043</property>
</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133625</id>
<property name="destinationPageTitle"><![CDATA[//www.mbari.org/pw]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
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<property name="creatorName"><![CDATA[carueda]]></property>
<property name="creationDate">2015-01-14 16:09:56.043</property>
<property name="lastModifierName"><![CDATA[carueda]]></property>
<property name="lastModificationDate">2015-01-14 16:09:56.043</property>
</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133624</id>
<property name="destinationPageTitle"><![CDATA[//en.wikipedia.org/wiki/PH]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
</property>
<property name="creatorName"><![CDATA[carueda]]></property>
<property name="creationDate">2015-01-14 16:09:56.043</property>
<property name="lastModifierName"><![CDATA[carueda]]></property>
<property name="lastModificationDate">2015-01-14 16:09:56.043</property>
</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133623</id>
<property name="destinationPageTitle"><![CDATA[H+]]></property>
<property name="destinationSpaceKey"><![CDATA[CLT]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
</property>
<property name="creatorName"><![CDATA[carueda]]></property>
<property name="creationDate">2015-01-14 16:09:56.043</property>
<property name="lastModifierName"><![CDATA[carueda]]></property>
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</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133622</id>
<property name="destinationPageTitle"><![CDATA[//en.wikipedia.org/wiki/Base_%28chemistry%29]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
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</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133621</id>
<property name="destinationPageTitle"><![CDATA[//en.wikipedia.org/wiki/Acid]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
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<property name="lastModificationDate">2015-01-14 16:09:56.043</property>
</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133620</id>
<property name="destinationPageTitle"><![CDATA[//en.wikipedia.org/wiki/Principal_components_analysis]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
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</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133650</id>
<property name="destinationPageTitle"><![CDATA[//en.wikipedia.org/wiki/Hardware]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
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<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133651</id>
<property name="destinationPageTitle"><![CDATA[//en.wikipedia.org/wiki/UART]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
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</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133648</id>
<property name="destinationPageTitle"><![CDATA[//www.tsa.gov/what_we_do/layers/twic/index.shtm]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
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<property name="creatorName"><![CDATA[carueda]]></property>
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</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133649</id>
<property name="destinationPageTitle"><![CDATA[//en.wikipedia.org/wiki/Computer]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
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</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133646</id>
<property name="destinationPageTitle"><![CDATA[//www.unidata.ucar.edu/projects/THREDDS/]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
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<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133647</id>
<property name="destinationPageTitle"><![CDATA[//www.unidata.ucar.edu/projects/THREDDS/]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
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<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133644</id>
<property name="destinationPageTitle"><![CDATA[//new-ssds.mbari.org:8080/ssds/]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
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<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133645</id>
<property name="destinationPageTitle"><![CDATA[//oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]]></property>
<property name="destinationSpaceKey"><![CDATA[https]]></property>
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<id name="id">27133642</id>
<property name="destinationPageTitle"><![CDATA[//www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
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<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133643</id>
<property name="destinationPageTitle"><![CDATA[//www.mbari.org/ssds/]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
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</object>
<object class="OutgoingLink" package="com.atlassian.confluence.links">
<id name="id">27133640</id>
<property name="destinationPageTitle"><![CDATA[//www.smdhydrovision.com]]></property>
<property name="destinationSpaceKey"><![CDATA[http]]></property>
<property name="sourceContent" class="Page" package="com.atlassian.confluence.pages"><id name="id">9372367</id>
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There are&nbsp;two recommended CVS Clients to access the MBARI CVS Respository including:&nbsp;{color:#ff0000}{*}WinCVS{*}{color} and {color:#ff0000}{*}SmartCVS{*}{color}.&nbsp;&nbsp; Both clients work for all major operating systems including Windows, Macintosh, and Linux systems.&nbsp;The key bits of information to use when setting up either client are the following:
* {color:#0000cc}Your access method needs to be set to&nbsp;{color}{color:#0000cc}{*}pserver{*}{color}{color:#0000cc}&nbsp;(SmartCVS) or{color} {color:#0000cc}{*}passwd file on server{*}{color} {color:#0000cc}(WinCVS){color}
* {color:#0000cc}User&nbsp; (Your MBARI user/e-mail&nbsp;account, e.g.,{color} {color:#0000cc}{_}salamy{_}{color}{color:#0000cc}){color}
* {color:#0000cc}Repository Server (MBARI CVS Repository is hosted on{color} {color:#0000cc}{*}{_}moonjelly{_}{*}{color}{color:#0000cc}){color}
* {color:#0000cc}CVSROOT ({color}{color:#0000cc}{*}_/home/cvs{_}{*}{color}{color:#0000cc}){color}

Thus, the full CVSROOT path for user _salamy_ would be:&nbsp;&nbsp;&nbsp; salamy@moonjelly:/home/cvs&nbsp;

----
\\

h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Windows-7.1.1.zip|^smartcvs-win32-setup-nojre-7_1_1.zip|SmartCVS Windows version 7.1.1] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOSX-7.1.1.tar.gz|^smartcvs-generic-7_1_1.tar.gz|SmartCVS Macintosh Version 7.1.1] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartSVN-Linux-7.1.tar.gz|^smartcvs-generic-7_1.tar.gz|SmartSVN Linux Version 7.1] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}({color}{color:#0066cc}{*}NOTE:*{color}{color:#0066cc}&nbsp;Setup same for MacCVS and gCVS as well){color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS Getting-Started Tutorial|^smartcvs-tutorial.pdf] \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-6.5.8.zip|^smartsvn-windows-x86-setup-nojre-6_5_8.zip|SmartSVN for Windows version 6.5.8]&nbsp;&nbsp; {color:#ff0000}*\- NEW\!*{color}

\\
\\
\\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-Mac-6.5.8.tar.gz|^smartsvn-macosx-6_5_5.tar.gz|SmartSVN Macintosh version 6.5.5]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}

\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-Linux-6.5.8.tar.gz|^smartsvn-generic-6_5_5.tar.gz|SmartSVN Linux version 6.5.5]&nbsp;{color:#ff0000}*\- NEW\!*{color}

\\
\\
\\
\\
\\
\\
\\
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-6.5.8.zip|^smartsvn-windows-x86-setup-nojre-6_5_8.zip|SmartSVN for Windows version 6.5.8]&nbsp;&nbsp; {color:#ff0000}*\- NEW\!*{color}

\\
\\
\\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-Mac-6.5.8.tar.gz|^smartsvn-macosx-6_5_8.tar.gz|SmartSVN Macintosh version 6.5.8]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}

\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-Linux-6.5.8.tar.gz|^smartsvn-generic-6_5_5.tar.gz|SmartSVN Linux version 6.5.5]&nbsp;{color:#ff0000}*\- NEW\!*{color}

\\
\\
\\
\\
\\
\\
\\
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There are&nbsp;two recommended CVS Clients to access the MBARI CVS Respository including:&nbsp;{color:#ff0000}{*}WinCVS{*}{color} and {color:#ff0000}{*}SmartCVS{*}{color}.&nbsp;&nbsp; Both clients work for all major operating systems including Windows, Macintosh, and Linux systems.&nbsp;The key bits of information to use when setting up either client are the following:
* {color:#0000cc}Your access method needs to be set to&nbsp;{color}{color:#0000cc}{*}pserver{*}{color}{color:#0000cc}&nbsp;(SmartCVS) or{color} {color:#0000cc}{*}passwd file on server{*}{color} {color:#0000cc}(WinCVS){color}
* {color:#0000cc}User&nbsp; (Your MBARI user/e-mail&nbsp;account, e.g.,{color} {color:#0000cc}{_}salamy{_}{color}{color:#0000cc}){color}
* {color:#0000cc}Repository Server (MBARI CVS Repository is hosted on{color} {color:#0000cc}{*}{_}moonjelly{_}{*}{color}{color:#0000cc}){color}
* {color:#0000cc}CVSROOT ({color}{color:#0000cc}{*}_/home/cvs{_}{*}{color}{color:#0000cc}){color}

Thus, the full CVSROOT path for user _salamy_ would be:&nbsp;&nbsp;&nbsp; salamy@moonjelly:/home/cvs&nbsp;

----
\\

h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Windows-7.1.zip|^smartcvs-win32-setup-nojre-7_1.zip|SmartCVS Windows version 7.1] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOSX-7.1.tar.gz|^smartcvs-macosx-7_1.tar.gz|SmartCVS Macintosh Version 7.1] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartSVN-Linux-7.1.tar.gz|^smartcvs-generic-7_1.tar.gz|SmartSVN Linux Version 7.1] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}({color}{color:#0066cc}{*}NOTE:*{color}{color:#0066cc}&nbsp;Setup same for MacCVS and gCVS as well){color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS Getting-Started Tutorial|^smartcvs-tutorial.pdf] \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

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h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

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There are&nbsp;two recommended CVS Clients to access the MBARI CVS Respository including:&nbsp;{color:#ff0000}{*}WinCVS{*}{color} and {color:#ff0000}{*}SmartCVS{*}{color}.&nbsp;&nbsp; Both clients work for all major operating systems including Windows, Macintosh, and Linux systems.&nbsp;The key bits of information to use when setting up either client are the following:
* {color:#0000cc}Your access method needs to be set to&nbsp;{color}{color:#0000cc}{*}pserver{*}{color}{color:#0000cc}&nbsp;(SmartCVS) or{color} {color:#0000cc}{*}passwd file on server{*}{color} {color:#0000cc}(WinCVS){color}
* {color:#0000cc}User&nbsp; (Your MBARI user/e-mail&nbsp;account, e.g.,{color} {color:#0000cc}{_}salamy{_}{color}{color:#0000cc}){color}
* {color:#0000cc}Repository Server (MBARI CVS Repository is hosted on{color} {color:#0000cc}{*}{_}moonjelly{_}{*}{color}{color:#0000cc}){color}
* {color:#0000cc}CVSROOT ({color}{color:#0000cc}{*}_/home/cvs{_}{*}{color}{color:#0000cc}){color}

Thus, the full CVSROOT path for user _salamy_ would be:&nbsp;&nbsp;&nbsp; salamy@moonjelly:/home/cvs&nbsp;

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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Windows-7.1.1.zip|^smartcvs-win32-setup-nojre-7_1_1.zip|SmartCVS Windows version 7.1.1] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOSX-7.1.tar.gz|^smartcvs-macosx-7_1.tar.gz|SmartCVS Macintosh Version 7.1] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartSVN-Linux-7.1.tar.gz|^smartcvs-generic-7_1.tar.gz|SmartSVN Linux Version 7.1] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}({color}{color:#0066cc}{*}NOTE:*{color}{color:#0066cc}&nbsp;Setup same for MacCVS and gCVS as well){color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS Getting-Started Tutorial|^smartcvs-tutorial.pdf] \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
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h3. *SmartSVN GUI Installation Files*


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h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-6.5.6.zip|^smartsvn-windows-x86-setup-nojre-6_5_6.zip|SmartSVN for Windows version 6.5.6]&nbsp;&nbsp; {color:#ff0000}*\- NEW\!*{color}

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h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-Mac-6.5.5.tar.gz|^smartsvn-macosx-6_5_5.tar.gz|SmartSVN Macintosh version 6.5.5]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}

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h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-Linux-6.5.5.tar.gz|^smartsvn-generic-6_5_5.tar.gz|SmartSVN Linux version 6.5.5]&nbsp;{color:#ff0000}*\- NEW\!*{color}

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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
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h3. *SmartSVN GUI Installation Files*


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h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-6.5.8.zip|^smartsvn-windows-x86-setup-nojre-6_5_6.zip|SmartSVN for Windows version 6.5.6]&nbsp;&nbsp; {color:#ff0000}*\- NEW\!*{color}

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h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-Mac-6.5.8.tar.gz|^smartsvn-macosx-6_5_5.tar.gz|SmartSVN Macintosh version 6.5.5]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}

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h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-Linux-6.5.8.tar.gz|^smartsvn-generic-6_5_5.tar.gz|SmartSVN Linux version 6.5.5]&nbsp;{color:#ff0000}*\- NEW\!*{color}

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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit their respective websites.

Contact Kevin Gomes [mailto:kgomes@mbari.org], Brian Schlining [mailto:brian@mbari.org] or Kent Headley [mailto:headley@mbari.org] with questions or permission requests for certain tools.

{tip:title=External Availability}
Please note that Confluence, JIRA, and Alfresco are all available outside the MBARI firewall and can have external collaborator accounts that are not MBARI accounts.  This was a desirable feature of these tools and allows us to externally collaborate without risking security breaches at MBARI.
{tip}

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.
----
h3. Authentication and Single Sign On With Crowd

[Crowd|http://www.atlassian.com/crowd] is an authentication tool that is developed by [Atlassian|http://www.atlassian.com] and is provided to MBARI under a community/non-profit license.  It provides an internal user database so we can create external user accounts that can then be linked to other applications such as JIRA and Confluence.  It also connects to our internal MBARI user database using LDAP so that MBARI users can have Single Sign on capability across multiple applications.

Links for Crowd at MBARI:
* [Crowd Web Application|http://oceana.mbari.org:8095/crowd]
* [Documentation of MBARI Crowd Installation|MBARI Crowd Installation]

----
h3. Content Management with [Alfresco|https://alfresco.mbari.org/alfresco]

Alfresco is a Content Management System (CMS) intended to replace the Project Library on Tornado as the repository for MBARI project documentation. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

{info:title=Accounting Creates Projects in Alfresco}
One of the main benefits of Alfresco is that it can interact with our accounting system in an automated fashion. Because of this, we have the accounting system currently creating project spaces and directory structures in Alfresco automatically.  This allows the accounting software to then export all accounting activity (PDFs of AMEX, PO's, etc.) to the Alfresco spaces automatically.
{info}

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password without using "shore\" in front) to see the project library materials. The *Projects* folder is the space that contains the content for projects at MBARI.

To create a short cut to the Projects folder (or any folder), enter that folder, then select "More Actions/View Details", then "Create Shortcut" (on the right side of the page).  This will create a shortcut that will be available in the "Shelf".  To view the shortcuts in your "Shelf", click on the down arrow next to "Navigtor" on the left hand sidebar menu, then select "Shelf" and you will see your created shortcuts.

Here are some useful links related to MBARI's installation of Alfresco:
* [Alfresco's Homepage|http://www.alfresco.com/]
* [Alfresco's Developer Home Page|http://wiki.alfresco.com/wiki/Main_Page]
* [Alfresco's Enterprise Customer Portal|https://network.alfresco.com/extranet/]
* [Deployment Information for MBARI's Alfresco Installation|Deployment Information]
* [Installation Notes]
* [alfresco.mbari.org Installation Notes]
* [alfresco-test.shore.mbari.org Installation Notes]

----
h3. WIKI Collaboration Pages ([Confluence|https://oceana.mbari.org/confluence])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

# [Confluence Installation Notes]

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts an externally accessable Maven repository at [https://oceana.mbari.org/maven2], an internal repository at [http://seaspray.shore.mbari.org:8082/archiva/repository/internal/] and a repository manager at [http://seaspray.shore.mbari.org:8082/archiva]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modeling with UML (JBuilder 2008 R2)

You can download JBuilder 2008 R2 from here:

[http://embarcadero.com/downloads/index.php]

Once downloaded and installed, you need to copy the following [.slip|https://alfresco.mbari.org/alfresco/webdav/Engineering/Tools/Collaboration%20Tools/JBuilder/concurrent_48444.slip] file to the:

JBUILDER_HOME/license

directory.

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - http://www.ietf.org/rfc/rfc2141.txt
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit their respective websites.

Contact Kevin Gomes [mailto:kgomes@mbari.org], Brian Schlining [mailto:brian@mbari.org] or Kent Headley [mailto:headley@mbari.org] with questions or permission requests for certain tools.

{tip:title=External Availability}
Please note that Confluence, JIRA, and Alfresco are all available outside the MBARI firewall and can have external collaborator accounts that are not MBARI accounts.  This was a desirable feature of these tools and allows us to externally collaborate without risking security breaches at MBARI.
{tip}

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.
----
h3. Authentication and Single Sign On With Crowd

[Crowd|http://www.atlassian.com/crowd] is an authentication tool that is developed by [Atlassian|http://www.atlassian.com] and is provided to MBARI under a community/non-profit license.  It provides an internal user database so we can create external user accounts that can then be linked to other applications such as JIRA and Confluence.  It also connects to our internal MBARI user database using LDAP so that MBARI users can have Single Sign on capability across multiple applications.

Links for Crowd at MBARI:
* [Crowd Web Application|http://oceana.mbari.org:8095/crowd]
* [Documentation of MBARI Crowd Installation|SPEPRJ:MBARI Crowd Installation]

----
h3. Content Management with [Alfresco|https://alfresco.mbari.org/alfresco]

Alfresco is a Content Management System (CMS) intended to replace the Project Library on Tornado as the repository for MBARI project documentation. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

{info:title=Accounting Creates Projects in Alfresco}
One of the main benefits of Alfresco is that it can interact with our accounting system in an automated fashion. Because of this, we have the accounting system currently creating project spaces and directory structures in Alfresco automatically.  This allows the accounting software to then export all accounting activity (PDFs of AMEX, PO's, etc.) to the Alfresco spaces automatically.
{info}

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password without using "shore\" in front) to see the project library materials. The *Projects* folder is the space that contains the content for projects at MBARI.

To create a short cut to the Projects folder (or any folder), enter that folder, then select "More Actions/View Details", then "Create Shortcut" (on the right side of the page).  This will create a shortcut that will be available in the "Shelf".  To view the shortcuts in your "Shelf", click on the down arrow next to "Navigtor" on the left hand sidebar menu, then select "Shelf" and you will see your created shortcuts.

Here are some useful links related to MBARI's installation of Alfresco:
* [Alfresco's Homepage|http://www.alfresco.com/]
* [Alfresco's Developer Home Page|http://wiki.alfresco.com/wiki/Main_Page]
* [Alfresco's Enterprise Customer Portal|https://network.alfresco.com/extranet/]
* [Deployment Information for MBARI's Alfresco Installation|Deployment Information]
* [Installation Notes]
* [alfresco.mbari.org Installation Notes]
* [alfresco-test.shore.mbari.org Installation Notes]

----
h3. WIKI Collaboration Pages ([Confluence|https://oceana.mbari.org/confluence])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

# [Confluence Installation Notes]

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts an externally accessable Maven repository at [https://oceana.mbari.org/maven2], an internal repository at [http://seaspray.shore.mbari.org:8082/archiva/repository/internal/] and a repository manager at [http://seaspray.shore.mbari.org:8082/archiva]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modeling with UML (JBuilder 2008 R2)

You can download JBuilder 2008 R2 from here:

[http://embarcadero.com/downloads/index.php]

Once downloaded and installed, you need to copy the following [.slip|https://alfresco.mbari.org/alfresco/webdav/Engineering/Tools/Collaboration%20Tools/JBuilder/concurrent_48444.slip] file to the:

JBUILDER_HOME/license

directory.

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[----
h3. *{+}Welcome to CVS\!+*

CVS is the MBARI Software Engineering source code repository which resides on the Linux server '{color:#3300ff}{_}moonjelly{_}{color}'.&nbsp;&nbsp;Someone has&nbsp;requested that you be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

h3. \\


h3. +Permissions+

Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout the project for security purposes.&nbsp;
\\
&nbsp;

h3. +Password Access+

Access to the repository requires another (_separate_) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network (_usually with the command prompt, Cygwin Window, or a Linux Terminal_) by logging in to moonjelly via {color:#3300ff}{*}ssh{*}{color} with your standard MBARI password (example: ssh salamy@moonjelly.shore.mbari.org).  This will run the script: &nbsp;{color:red}{*}encryptCVSpw{*}{color}
Follow the instructions in order to output an encrypted version of your password.&nbsp; You may put any password in that you wish - even the same one as your standard MBARI network password.&nbsp; That is up to you.  The system will then email you a copy of your encrypted password to you.  

*{+}Please forward that e-mail to me+* so that I may add/update your password to the repository password list.&nbsp; I will then send you an e-mail when you are able to access the repository.

NOTE:_moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot access _moonjelly_ for any reason, please let me know.
\\
&nbsp;

h3. *{+}CVS GUIs{+}*

GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the link [Setting up WinCVS_1.2|^Setting_up_WinCVS_1.2_new.doc]. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. Please&nbsp;remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

Regards, - Karen A. Salamy (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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<property name="body"><![CDATA[----
h3. *{+}Welcome to CVS\!+*

CVS is the MBARI Software Engineering source code repository which resides on the Linux server '{color:#3300ff}{_}moonjelly{_}{color}'.&nbsp;&nbsp;Someone has&nbsp;requested that you be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

h3. \\


h3. +Permissions+

Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout the project for security purposes.&nbsp;
\\
&nbsp;

h3. +Password Access+

Access to the repository requires another (_separate_) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network (_usually with the command prompt, Cygwin Window, or a Linux Terminal_), login to moonjelly via {color:#3300ff}{*}ssh{*}{color} with your standard MBARI password (example: ssh salamy@moonjelly.shore.mbari.org).  This will run the script: &nbsp;{color:red}{*}encryptCVSpw{*}{color}
Follow the instructions in order to output an encrypted version of your password.&nbsp; You may put any password in that you wish - even the same one as your standard MBARI network password.&nbsp; That is up to you.  The system will then email you a copy of your encrypted password to you.  

*{+}Please forward that e-mail to me+* so that I may add/update your password to the repository password list.&nbsp; I will then send you an e-mail when you are able to access the repository.

NOTE:_moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot access _moonjelly_ for any reason, please let me know.
\\
&nbsp;

h3. *{+}CVS GUIs{+}*

GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the link [Setting up WinCVS_1.2|^Setting_up_WinCVS_1.2_new.doc]. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. Please&nbsp;remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

Regards, - Karen A. Salamy (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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<property name="body"><![CDATA[----
h3. *{+}Welcome to CVS\!+*

CVS is the MBARI Software Engineering source code repository which resides on the Linux server '{color:#3300ff}{_}moonjelly{_}{color}'.&nbsp;&nbsp;Someone has&nbsp;requested that you be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

h3. \\


h3. +Permissions+

Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout the project for security purposes.&nbsp;
\\
&nbsp;

h3. +Password Access+

Access to the repository requires another (_separate_) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network (_usually with the command prompt, Cygwin Window, or a Linux Terminal_) by logging in to moonjelly via {color:#3300ff}{*}ssh{*}{color} with your standard MBARI password (example: ssh salamy@moonjelly.shore.mbari.org).  This will run the script: &nbsp;{color:red}{*}encryptCVSpw{*}{color}

Follow the onscreen instructions to create an encrypted version of your password.&nbsp; You may put any password in that you wish - even the same one as your standard MBARI network password.&nbsp; That is up to you.  The system will then email you a copy of your encrypted password.  *{+}Please forward that e-mail to me+* so that I may add/update your password to the repository password list.&nbsp; I will then send you an e-mail when you are able to access the repository.

NOTE:_moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot access _moonjelly_ for any reason, please let me know.
\\
&nbsp;

h3. *{+}CVS GUIs{+}*

GUIs are the main way users interact with the repository to checkout, edit, and checkin files. I highly recommend the "Free" [SmartCVS Client|http://www.syntevo.com/smartcvs/download|Download SmartCVS Client] version to access moonjelly.  However, there are many other clients including WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) should you prefer them. You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the link [Setting up WinCVS_1.2|^Setting_up_WinCVS_1.2_new.doc]. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. Please&nbsp;remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

Regards, - Karen A. Salamy (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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<property name="body"><![CDATA[----
h3. *{+}Welcome to CVS\!+*

CVS is the MBARI Software Engineering source code repository which resides on the Linux server '{color:#3300ff}{_}moonjelly{_}{color}'.&nbsp;&nbsp;Someone has&nbsp;requested that you be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

h3. \\


h3. +Permissions+

Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout the project for security purposes.&nbsp;
\\
&nbsp;

h3. +Password Access+

Access to the repository requires another (_separate_) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network (_usually with the command prompt, Cygwin Window, or a Linux Terminal_) by logging in to moonjelly via {color:#3300ff}{*}ssh{*}{color} with your standard MBARI password (example: ssh salamy@moonjelly.shore.mbari.org).  This will run the script: &nbsp;{color:red}{*}encryptCVSpw{*}{color}

Follow the onscreen instructions to create an encrypted version of your password.&nbsp; You may put any password in that you wish - even the same one as your standard MBARI network password.&nbsp; That is up to you.  The system will then email you a copy of your encrypted password.  *{+}Please forward that e-mail to me+* so that I may add/update your password to the repository password list.&nbsp; I will then send you an e-mail when you are able to access the repository.

NOTE:_moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot access _moonjelly_ for any reason, please let me know.
\\
&nbsp;

h3. *{+}CVS GUIs{+}*

GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the link [Setting up WinCVS_1.2|^Setting_up_WinCVS_1.2_new.doc]. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. Please&nbsp;remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

Regards, - Karen A. Salamy (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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<property name="body"><![CDATA[----
h3. *{+}Welcome to CVS\!+*

CVS is the MBARI Software Engineering source code repository which resides on the Linux server '{color:#3300ff}{_}moonjelly{_}{color}'.&nbsp;&nbsp;Someone has&nbsp;requested that you be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

h3. \\


h3. +Permissions+

Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout the project for security purposes.&nbsp;
\\
&nbsp;

h3. +Password Access+

Access to the repository requires another (_separate_) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network (_usually with the command prompt, Cygwin Window, or a Linux Terminal_) by logging in to moonjelly via {color:#3300ff}{*}ssh{*}{color} with your standard MBARI password (example: ssh salamy@moonjelly.shore.mbari.org).  This will run the script: &nbsp;{color:red}{*}encryptCVSpw{*}{color}

Follow the onscreen instructions to create an encrypted version of your password.&nbsp; You may put any password in that you wish - even the same one as your standard MBARI network password.&nbsp; That is up to you.  The system will then email you a copy of your encrypted password.  *{+}Please forward that e-mail to me+* so that I may add/update your password to the repository password list.&nbsp; I will then send you an e-mail when you are able to access the repository.

NOTE:_moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot access _moonjelly_ for any reason, please let me know.
\\
&nbsp;

h3. *{+}CVS GUIs{+}*

GUIs are the main way users interact with the repository to checkout, edit, and checkin files. I highly recommend the "Free" [SmartCVS Client|http://www.syntevo.com/smartcvs/download|Download SmartCVS Client] to access moonjelly.  However, there are many other clients including WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) should you prefer them. You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the link [Setting up WinCVS_1.2|^Setting_up_WinCVS_1.2_new.doc]. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. Please&nbsp;remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

Regards, - Karen A. Salamy (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools

h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed. 

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool.  It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant.  You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory.

{note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above).  You can still use Together, but we are not eligible for upgrade/patches.
{note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

{warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN{code}{warning}

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.]]></property>
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<property name="body"><![CDATA[----
h3. *{+}Welcome to CVS\!+*

CVS is the MBARI Software Engineering source code repository which resides on the Linux server '{color:#3300ff}{_}moonjelly{_}{color}'.&nbsp;&nbsp;Someone has&nbsp;requested that you be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

h3. \\


h3. +Permissions+

Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout the project for security purposes.&nbsp;
\\
&nbsp;

h3. +Password Access+

Access to the repository requires another (_separate_) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network (_usually with the command prompt, Cygwin Window, or a Linux Terminal_), {color:#3300ff}{*}telnet{*}{color} and login to _moonjelly_ with your standard MBARI password and type the following at the prompt: &nbsp;{color:red}{*}encryptCVSpw{*}{color}
This runs a script that outputs an encrypted version of your password.&nbsp; You may put any password in that you wish - even the same one as your standard MBARI network password.&nbsp; That is up to you.

Next, *{+}Please e-mail me the encrypted text (exactly as shown)+* so that I may add you to the repository password list.&nbsp; I will send you an e-mail when you are able to access the repository.

NOTE:_moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot access _moonjelly_ for any reason, please let me know.
\\
&nbsp;

h3. *{+}CVS GUIs{+}*

GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the link [Setting up WinCVS_1.2|^Setting_up_WinCVS_1.2_new.doc]. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. Please&nbsp;remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

Regards, - Karen A. Salamy (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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<property name="body"><![CDATA[h2. About Jar Signing

If you intend to distribute an application using Java Web Start you will need to digitally sign the jar using a certificate that verifies the jars origin. MBARI provides a security certificate from [Verisign|http://www.verisign.com/] that you can use for signing your Java applications.

h3. Keystore Details

||Parameter||value||
|Keystore location|[http://seaspray.shore.mbari.org/keystore/keystore.bin]|
|Keystore Alias|MBARIjava|
|Keystore Password|java1700|
|Key Password|javaBeansMakeLousyCoffee|

h3. Ant Example

Here's an example of how to sign your jars using [Ant|http://ant.apache.org/]

{code:xml}
<target name="sign" description="Sign jar files" >
    <property name="lib" value="lib" />
    <property name="keystore.alias" value="MBARIjava" />
    <property name="keystore.passwd" value="java1700" />
    <property name="key.password" value="javaBeansMakeLousyCoffee" />
    <property name="keystore" value="http://seaspray.shore.mbari.org/keystore/keystore.bin" />
    <signjar alias="${keystore.alias}" storepass="${keystore.passwd}" keystore="${keystore}" keypass="${key.password}">
        <fileset dir="${lib}">
            <include name="**/*.jar" />
        </fileset>
    </signjar>
</target>
{code}]]></property>
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<property name="body"><![CDATA[h2. About Jar Signing

If you intend to distribute an application using Java Web Start you will need to digitally sign the jar using a certificate that verifies the jars origin. MBARI provides a security certificate from [Verisign|http://www.verisign.com/].

h3. Details

||Parameter||value||
|Keystore location|[http://seaspray.shore.mbari.org/keystore/keystore.bin]|
|Keystore Alias|MBARIjava|
|Keystore Password|java1700|
|Key Password|javaBeansMakeLousyCoffee|

h3. Ant Example

{code:xml}
<target name="sign" description="Sign jar files" >
    <property name="keystore.alias" value="MBARIjava" />
    <property name="keystore.passwd" value="java1700" />
    <property name="key.password" value="javaBeansMakeLousyCoffee" />
    <property name="keystore" value="http://seaspray.shore.mbari.org/keystore/keystore.bin" />
    <signjar alias="${keystore.alias}" storepass="${keystore.passwd}" keystore="${keystore}" keypass="${key.password}">
        <fileset dir="${lib}">
            <include name="**/*.jar" />
        </fileset>
    </signjar>
</target>
{code}]]></property>
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<property name="body"><![CDATA[h2. About Jar Signing

If you intend to distribute an application using Java Web Start you will need to digitally sign the jar using a certificate that verifies the jars origin. MBARI provides a security certificate from [Verisign|http://www.verisign.com/].

h3. Details

||Parameter||value||
|Keystore location|[http://seaspray.shore.mbari.org/keystore/keystore.bin]|
|Keystore Alias|MBARIjava|
|Keystore Password|java1700|
|Key Password|javaBeansMakeLousyCoffee|

h3. Ant Example

{code:xml}
<target name="sign" description="Sign jar files" >
    <property name="lib" value="lib" />
    <property name="keystore.alias" value="MBARIjava" />
    <property name="keystore.passwd" value="java1700" />
    <property name="key.password" value="javaBeansMakeLousyCoffee" />
    <property name="keystore" value="http://seaspray.shore.mbari.org/keystore/keystore.bin" />
    <signjar alias="${keystore.alias}" storepass="${keystore.passwd}" keystore="${keystore}" keypass="${key.password}">
        <fileset dir="${lib}">
            <include name="**/*.jar" />
        </fileset>
    </signjar>
</target>
{code}]]></property>
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<property name="body"><![CDATA[h2. About Jar Signing

If you intend to distribute an application using Java Web Start you will need to digitally sign the jar using a certificate that verifies the jars origin. MBARI provides a security certificate from [Verisign|http://www.verisign.com/]. The security certificate is currently located at [http://seaspray.shore.mbari.org/keystore/keystore.bin]

h3. Details

||Parameter||value||
|Keystore location|[http://seaspray.shore.mbari.org/keystore/keystore.bin]|
|Keystore Alias|MBARIjava|
|Keystore Password|java1700|
|Key Password|javaBeansMakeLousyCoffee|]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools

h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed. 

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool.  It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant.  You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory.

{note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above).  You can still use Together, but we are not eligible for upgrade/patches.
{note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

{warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN{code}{warning}

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.]]></property>
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\\
&nbsp;

h3. *SmartSVN GUI Installation Files*

* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|^SmartSVN.zip]\\ \\ \\]]></property>
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h3. *WinCVS GUI Installation Files & Set-Up Instructions*

* [WinCVS-1.2.0.zip|~salamy:Helpful Software Downloads^WinCvs120.zip]
* [Setting up WinCVS-1.2.0.pdf|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]
* [CVS Administrative Resource.doc - PASSWORD REQUIRED|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc]

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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.]]></property>
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h3. *WinCVS GUI Installation Files & Set-Up Instructions*

* [WinCVS-1.2.0.zip|^WinCvs120.zip]
* [Setting up WinCVS-1.2.0.pdf|^Setting up WinCVS_1 2.pdf]
* [CVS Administrative Resource.doc - PASSWORD REQUIRED|^CVS Source Code Repository.doc]

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h3. *WinCVS GUI Installation Files & Set-Up Instructions*

* [WinCVS-1.2.0.zip|~salamy:Helpful Software Downloads^WinCvs120.zip][WinCVS-1.2.0.zip|^WinCvs120.zip]
* [Setting up WinCVS-1.2.0.pdf|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf][Setting up WinCVS-1.2.0.pdf|^Setting up WinCVS_1 2.pdf]
* [CVS Administrative Resource.doc - PASSWORD REQUIRED|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc][CVS Administrative Resource.doc - PASSWORD REQUIRED|^CVS Source Code Repository.doc]

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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;. The most common CVS client at MBARI isAdditional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].

h3. &nbsp;&nbsp;


h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].

h3. &nbsp;&nbsp;


h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools

h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed. 

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool.  It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant.  You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory.

{note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above).  You can still use Together, but we are not eligible for upgrade/patches.
{note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

{warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN{code}{warning}

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI] ]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">3180110</id>
<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory.{note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches.{note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.{warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}

h3. Concurrent Versioning System


h3. &nbsp;


h3. &nbsp;&nbsp;


h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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h3. *WinCVS GUI Installation Files & Set-Up Instructions*

* [WinCVS-1.2.0.zip|~salamy:Helpful Software Downloads^WinCvs120.zip]
* [Setting up WinCVS-1.2.0.pdf|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]
* [CVS Administrative Resource.doc - PASSWORD REQUIRED|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc]

\\
&nbsp;]]></property>
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h3. *WinCVS GUI Installation Files &*

* [WinCVS-1.2.0.zip|~salamy:Helpful Software Downloads^WinCvs120.zip]\\

h3. WinCVS Set-Up Instructions

* [Setting up WinCVS-1.2.0.pdf|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]\\

h3. CVS Administrative Information - Access restricted

* [CVS Administrative Resource.doc - PASSWORD REQUIRED|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc]

\\
&nbsp;]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.

h3. &nbsp;Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].

h3. &nbsp;&nbsp;


h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">3180118</id>
<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\ \\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.

\\
&nbsp;

h3. &nbsp;Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.\\

h3. &nbsp;Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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h3. *CVS Client&nbsp;Files*

* [WinCVS-1.2.0.zip|~salamy:Helpful Software Downloads^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. WinCVS Set-Up Instructions

* [Setting up WinCVS-1.2.0.pdf|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]\\

h3. CVS Administrative Information

* [CVS Source Code Repository.doc - PASSWORD REQUIRED|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc]

\\
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h3. *CVS Client&nbsp;Files*

* [WinCVS-1.2.0.zip|~salamy:Helpful Software Downloads^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. WinCVS Set-Up Instructions

* [Setting up WinCVS-1.2.0.pdf|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]\\

h3. CVS Administrative Information

* [CVS Source Code Repository.doc - PASSWORD REQUIRED|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc][]

\\
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h3. *CVS Client&nbsp;Files*

* [WinCVS-1.2.0.zip|~salamy:Helpful Software Downloads^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* &nbsp;

h3. &nbsp;


h3. WinCVS Set-Up Instructions

* [Setting up WinCVS-1.2.0.pdf|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]\\

h3. &nbsp;


h3. CVS Administrative Information

* [CVS Source Code Repository.doc - {color:#ff0000}PASSWORD REQUIRED{color}|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc]

\\
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h3. *CVS Client&nbsp;Files*

* [WinCVS-1.2.0.zip|~salamy:Helpful Software Downloads^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. WinCVS Set-Up Instructions

* [Setting up WinCVS-1.2.0.pdf|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]\\

h3. CVS Administrative Information

* [CVS Administrative Resource.doc - {color:#ff0033}PASSWORD REQUIRED{color}|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc]

\\
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h3. *CVS Client&nbsp;Files*

* [WinCVS-1.2.0.zip|~salamy:Helpful Software Downloads^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. WinCVS Set-Up Instructions

* [Setting up WinCVS-1.2.0.pdf|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]\\

h3. CVS Administrative Information - Access restricted

* [CVS Administrative Resource.doc - PASSWORD REQUIRED|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc]

\\
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h3. *CVS Client&nbsp;Files*

* [WinCVS-1.2.0.zip|~salamy:Helpful Software Downloads^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. WinCVS Set-Up Instructions

* [Setting up WinCVS-1.2.0.pdf|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]\\

h3. CVS Administrative Information

* [CVS Administrative Resource.doc - {color:#ff0033}PASSWORD REQUIRED{color}|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc]

\\
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - http://ican.science.oregonstate.edu/home
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang= 
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
\\
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
\\
\\
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp; The CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/ .

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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h3. *CVS Client&nbsp;Installation Files*

* [WinCVS-1.2.0.zip|~salamy:Helpful Software Downloads^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}

h3. &nbsp;


h3. CVS Client Set-Up Instructions

* [Setting up WinCVS-1.2.0.pdf|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]\\

h3. &nbsp;


h3. CVS Administrative Information

* [CVS Admin Notes.doc|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
&nbsp;]]></property>
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h3. *CVS Client&nbsp;Files*

* [WinCVS-1.2.0.zip|~salamy:Helpful Software Downloads^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}

h3. &nbsp;


h3. WinCVS Set-Up Instructions

* [Setting up WinCVS-1.2.0.pdf|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]\\

h3. &nbsp;


h3. CVS Administrative Information

* [CVS Admin Notes.doc|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc]

\\
&nbsp;]]></property>
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h3. *CVS Client&nbsp;Installation Files*

* [WinCVS-1.2.0.zip|~salamy:Helpful Software Downloads^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}

h3. &nbsp;


h3. CVS Client Set-Up Instructions

* [Setting up WinCVS-1.2.0.pdf|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]\\

h3. &nbsp;


h3. CVS Administrative Information

* [CVS Admin Notes.doc|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc]

\\
&nbsp;]]></property>
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h3. *CVS Client&nbsp;Files*

* [WinCVS-1.2.0.zip|~salamy:Helpful Software Downloads^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}

h3. &nbsp;


h3. WinCVS Set-Up Instructions

* [Setting up WinCVS-1.2.0.pdf|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]\\

h3. &nbsp;


h3. CVS Administrative Information

* [PASSWORD REQUIRED|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc">CVS Source Code Repository.doc -PASSWORD REQUIRED]

\\
&nbsp;]]></property>
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\
\\
{color:blue}{*}Creating a project{*}{color} Due to the need for proper organization of files and file permissions, ALL projects

(_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository

administrator. Set-up involves creating project groups to restrict unauthorized users from editing or

destroying files. New repository projects (modules) are generally set-up at the request of project

managers, although any person who wishes to use the repository can make a request for a new

project. To have a project (module) created, please e-mail the desired project name and list of users

who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects

are _tiburon_, _isi_, _nmc_.{color:blue}*&nbsp;*{color}]]></property>
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\
{color:blue}{*}Creating a project.*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.]]></property>
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Here's the standard method of adding a new directory to the subversion repository.\\ \\ \\]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\
\\
\\
\\
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software Integration).&nbsp;
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">13926708</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">13959467</id>
<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
\\
\\
\\
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\
\\
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp; The CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
\\
\\
\\
\\
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\
\\
\\
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.\\

*Checking out a module.* To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.

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Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.]]></property>
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Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:*{color}

Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.]]></property>
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

\\
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

&nbsp;To add a new file to a directory, follow these steps:Step 1: You must first have a working copy of the directory (See item # 7).Step 2: Create the new file(s) inside your checked-out working copy of the directory.Step 3: In WinCVS, use the explore window (usually in left upper corner of screen) tobrowse to your home directory and view the new file(s) you have added. Clickthe new file(s) with your mouse and add the file(s) by either:1) Clicking on menu bar *Modify - Add Selection*. If the file contains binary dataclick *Modify - Add Selection Binary*. OR2) Clicking on the user interface button (white rectangle with a red "plus" sign onit). If the file is a binary, click the binary add button which is white with a red"plus" sign and 01 on it.NOTE: (Holding the shift key down allows the addition of more than one file at a time).Step 4: Commit the selection. This step actually "Adds" (checks-in) the file(s) to therepository. This can either be done with the file menu or with the user interfacebutton.1) Clicking on menu bar *Modify - Commit Selection*. OR{color:black}{*}2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color}{color:black}left on it).{color}{color:black}{*}NOTE:*{color} {color:black}(Holding the shift key down allows the addition of more than one file at a time).{color}{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color}{color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color}{color:black}are not recursive.{color}
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Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.

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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# ADCP: Acoustic Doppler Current Profiler - a sonar that attempts to produce a record of water current velocities for a range of depths [http://en.wikipedia.org/wiki/Acoustic_Doppler_Current_Profiler]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AMQP: Advanced Message Queuing Protocol - [http://www.amqp.org]
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ARI-WG: Access to Remote Instrumentation in a distributed environment - Working Group. OpenGrid Forum [http://www.ogf.org/gf/group_info/view.php?group=ari-wg]
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EarthCube: EarthCube is a NSF activity to create a data and knowledge management system for the 21st Century. The scientific objective is to develop a framework over the next decade to understand and predict the Earth system from the sun to the center of the Earth [http://earthcube.ning.com/]
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# HDF: Hierarchical Data Format
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# JVM: Java Virtual Machine - [http://en.wikipedia.org/wiki/Jvm]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MB/CA Current: a MBARI project in 2011
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NODC: National Oceanographic Data Center - http://www.nodc.noaa.gov/
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# ODSS: Oceanographic Decision Support System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOI CI: Ocean Observatories Initiative CyberInfrastructure: [http://ci.oceanobservatories.org/] (Developers site: [http://ooici.net/])
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software).
# SCPI: Self Contained Plankton Imager, an MBARI project in 2011
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WCS: Web Coverage Service
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

{note:title=Test Machine Installation Difference}
I also setup a test machine to help Alan Lash have something to develop against and for me to test somethings like using MS SQL Server instead of my SQL.  I will write notes where the instructions differ.  I setup the test machine on ssdsdevpc.shore.mbari.org which is an HP desktop machine running Fedora Core 7.
{note}

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 (tomcat version) from alfresco.org (the tar.gz file and moved it to /opt)
{note:title=Test Machine Installation Difference}
On the test machine, I installed Alfresco 2.1 tomcat version
{note}
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
{note:title=Test Machine Installation Difference}
I.S. was hoping to get Alfresco to run against the institutes MS SQL Server for support reasons so on the test machine, I used a database named 'Alfresco' on our database server solstice.shore.mbari.org.  Neil created the database for me and the user DB_Collaboration was used to access it.
{note}
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
{note:title=Test Machine Installation Difference}
Fedora core 7 had 5.2.2 installed
{note}
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
{note:title=Test Machine Installation Difference}
I named the directory alfresco-2.1
{note}
# I then moved the tar into the alfresco-2.0 directory
{note:title=Test Machine Installation Difference}
alfreso-2.1 directory
{note}
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
{note:title=Test Machine Installation Difference}
This was a bit different in FC7.  In order to get Xvfb installed I used "Add/Remove Software" to install it.  OpenOffice was already installed so I just had to find the soffice command location.  The command to get Xvfb running was also a bit different.  I had to create a ascii file called /etc/xvfb-auth.cfg that only had one line in it that read 'localhost'.  Then the command to start Xvfb was 'Xvfb :1 -auth /etc/xvfb-auth.cfg'.  Then I could start soffice the same way.  I changed the start_oo.sh file to reflect those commands.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
{note:title=Test Machine Installation Difference}
Did not do this
{note}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
{note:title=Test Machine Installation Difference}
/data/alfresco-2.1
{note}
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
{note:title=Test Machine Installation Difference}
This file already existed and was no different from the sample, so I skipped this step
{note}
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
{note:title=Test Machine Installation Difference}
This file already existed and so copied the original to custom-repository.properties.orig and edited the existing one.
{note}
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
{note:title=Test Machine Installation Difference}
I changed them to work with the MS SQL Server login so they looked like:
db.username=DB_Collaboration
db.password=********
db.pool.initial=10
db.pool.max=100
{note}
### I commented out the two HSQL connection lines
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
{note:title=Test Machine Installation Difference}
Left the MySQL lines commented out, but uncommented the SQLServer lines and changed them to
db.driver=net.sourceforge.jtds.jdbc.Driver
db.url=jdbc:jtds:sqlserver://solstice.shore.mbari.org/Alfresco;domain=SHORE;user=DB_Collaboration;password=******
{note}
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
{note:title=Test Machine Installation Difference}
Already existed, so backuped up to .orig and edited to comment out the HSQL and uncomment the SQLServer one.
{note}
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
{note:title=Test Machine Installation Difference}
The downloaded alfresco already has the MySQL driver jar in the install, but since I am using SQLServer, I downloaded the jtds driver from the internet and installed the jtds-X.X.X.jar file in the /opt/alfresco-2.1/tomcat/common/lib to make it available to alfresco.
{note}
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0.  I also added the following line after the line that stated 'killall soffice.bin':
killall Xvfb.  That ensured the Xvfb process was killed when alfresco was shutdown.
{note:title=Test Machine Installation Difference}
Set it to /opt/alfresco-2.1/tomcat for the test machine
{note}
{tip}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{tip}
{note:title=Test Machine Installation Difference}
For the test machine, I wasn't too worried about details, so I skipped the next 15 or so steps (picks up again at configuring for MBARI LDAP below.
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{tip}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{tip}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{tip}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{tip}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## We wanted to be able to make sure we could have collaborator accounts that were not MBARI LDAP accounts so that we could have Alfresco users that had not permissions at all on the MBARI network.  In order to do this, I used the Alfresco native user service and chained the authentication together with the MBARI LDAP.  In order to do this, I copied the chaining-authentication-context.xml.sample to chaining-authentication-context.xml.  I then edited the file to make the appropriate changes (I have also attached the changed config file here for downloading):
### The first change was to the first bean declaration's id from *authenticationServiceImpl* to *authenticationService*.
### In the same bean declaration, I changed the first authentication services reference from *authenticationServiceImplJAAS* to *authenticationServiceImplLDAP* 
### I then changed the JAAS bean declaration to point to the ldap declaration by changing the bean id from *authenticationServiceImplJAAS* to *authenticationServiceImplLDAP*
### There are two properties in this bean and I had to change them to point to the LDAP configuration (these changes actually reference the services defined in the ldap-authentication-context.xml configuration file).
#### Change the authenticationDao property's value from *authenticationDaoJAAS* to *authenticationDaoLDAP*
#### Change the authenticationComponent property from *authenticationComponentImplJAAS* to *authenticationComponentImplLDAP*
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponent" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
{note:title=Test Machine Installation Difference}
Did not setup SSL for the test machine
{note}
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{tip}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{tip}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

{note:title=Test Machine Installation Difference}
I also setup a test machine to help Alan Lash have something to develop against and for me to test somethings like using MS SQL Server instead of my SQL.  I will write notes where the instructions differ.  I setup the test machine on ssdsdevpc.shore.mbari.org which is an HP desktop machine running Fedora Core 7.
{note}

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 (tomcat version) from alfresco.org (the tar.gz file and moved it to /opt)
{note:title=Test Machine Installation Difference}
On the test machine, I installed Alfresco 2.1 tomcat version
{note}
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
{note:title=Test Machine Installation Difference}
I.S. was hoping to get Alfresco to run against the institutes MS SQL Server for support reasons so on the test machine, I used a database named 'Alfresco' on our database server solstice.shore.mbari.org.  Neil created the database for me and the user DB_Collaboration was used to access it.
{note}
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
{note:title=Test Machine Installation Difference}
Fedora core 7 had 5.2.2 installed
{note}
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
{note:title=Test Machine Installation Difference}
I named the directory alfresco-2.1
{note}
# I then moved the tar into the alfresco-2.0 directory
{note:title=Test Machine Installation Difference}
alfreso-2.1 directory
{note}
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
{note:title=Test Machine Installation Difference}
This was a bit different in FC7.  In order to get Xvfb installed I used "Add/Remove Software" to install it.  OpenOffice was already installed so I just had to find the soffice command location.  The command to get Xvfb running was also a bit different.  I had to create a ascii file called /etc/xvfb-auth.cfg that only had one line in it that read 'localhost'.  Then the command to start Xvfb was 'Xvfb :1 -auth /etc/xvfb-auth.cfg'.  Then I could start soffice the same way.  I changed the start_oo.sh file to reflect those commands.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
{note:title=Test Machine Installation Difference}
Did not do this
{note}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
{note:title=Test Machine Installation Difference}
/data/alfresco-2.1
{note}
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
{note:title=Test Machine Installation Difference}
This file already existed and was no different from the sample, so I skipped this step
{note}
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
{note:title=Test Machine Installation Difference}
This file already existed and so copied the original to custom-repository.properties.orig and edited the existing one.
{note}
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
{note:title=Test Machine Installation Difference}
I changed them to work with the MS SQL Server login so they looked like:
db.username=DB_Collaboration
db.password=********
db.pool.initial=10
db.pool.max=100
{note}
### I commented out the two HSQL connection lines
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
{note:title=Test Machine Installation Difference}
Left the MySQL lines commented out, but uncommented the SQLServer lines and changed them to
db.driver=net.sourceforge.jtds.jdbc.Driver
db.url=jdbc:jtds:sqlserver://solstice.shore.mbari.org/Alfresco;domain=SHORE;user=DB_Collaboration;password=******
{note}
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
{note:title=Test Machine Installation Difference}
Already existed, so backuped up to .orig and edited to comment out the HSQL and uncomment the SQLServer one.
{note}
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
{note:title=Test Machine Installation Difference}
The downloaded alfresco already has the MySQL driver jar in the install, but since I am using SQLServer, I downloaded the jtds driver from the internet and installed the jtds-X.X.X.jar file in the /opt/alfresco-2.1/tomcat/common/lib to make it available to alfresco.
{note}
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0.  I also added the following line after the line that stated 'killall soffice.bin':
killall Xvfb.  That ensured the Xvfb process was killed when alfresco was shutdown.
{note:title=Test Machine Installation Difference}
Set it to /opt/alfresco-2.1/tomcat for the test machine
{note}
{tip}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{tip}
{note:title=Test Machine Installation Difference}
For the test machine, I wasn't too worried about details, so I skipped the next 15 or so steps (picks up again at configuring for MBARI LDAP below.
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{tip}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{tip}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{tip}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{tip}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponent" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
{note:title=Test Machine Installation Difference}
Did not setup SSL for the test machine
{note}
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{tip}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{tip}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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<property name="body"><![CDATA[\\

There are&nbsp;two recommended CVS Clients to access the MBARI CVS Respository including:&nbsp;{color:#ff0000}{*}WinCVS{*}{color} and {color:#ff0000}{*}SmartCVS{*}{color}.&nbsp;&nbsp; Both clients work for all major operating systems including Windows, Macintosh, and Linux systems.&nbsp;The key bits of information to use when setting up either client are the following:
* {color:#0000cc}Your access method needs to be set to&nbsp;{color}{color:#0000cc}{*}pserver{*}{color}{color:#0000cc}&nbsp;(SmartCVS) or{color} {color:#0000cc}{*}passwd file on server{*}{color} {color:#0000cc}(WinCVS){color}
* {color:#0000cc}User&nbsp; (Your MBARI user/e-mail&nbsp;account, e.g.,{color} {color:#0000cc}{_}salamy{_}{color}{color:#0000cc}){color}
* {color:#0000cc}Repository Server (MBARI CVS Repository is hosted on{color} {color:#0000cc}{*}{_}moonjelly.shore.mbari.org{_}{*}{color}{color:#0000cc}){color}
* {color:#0000cc}CVSROOT ({color}{color:#0000cc}{*}_/home/cvs{_}{*}{color}{color:#0000cc}){color}

Thus, the full CVSROOT path for user _salamy_ would be:&nbsp;&nbsp;&nbsp; salamy@moonjelly.shore.mbari.org:/home/cvs&nbsp;

----
\\

h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Windows-7.1.3.zip|^smartcvs-win32-setup-nojre-7_1_3.zip|SmartCVS Windows version 7.1.3] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOSX-7.1.3.tar.gz|^smartcvs-macosx-7_1_3.tar.gz|SmartCVS Macintosh Version 7.1.3] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-7.1.3.tar.gz|^smartcvs-generic-7_1_3.tar.gz|SmartSVN Linux Version 7.1.3] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}({color}{color:#0066cc}{*}NOTE:*{color}{color:#0066cc}&nbsp;Setup same for MacCVS and gCVS as well){color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS Getting-Started Tutorial|^smartcvs-tutorial.pdf] \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
&nbsp;]]></property>
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

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h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-7.0.1.zip|^smartsvn-windows-x86-setup-nojre-7_0_1.zip|SmartSVN for Windows Version 7.0.1]&nbsp;&nbsp; {color:#ff0000}*\- NEW\!*{color}

\\
\\
\\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-Mac-7.0.1.tar|^smartsvn-macosx-7_0_1.tar.gz|SmartSVN Macintosh version 7.0.1]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}

\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-Linux-7.0.1.tar.gz|^smartsvn-generic-7_0_1.tar.gz|SmartSVN for Linux Version 7.0.1]&nbsp;{color:#ff0000}*\- NEW\!*{color}

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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-7.0.1.zip|^smartsvn-windows-x86-setup-nojre-7_0_1.zip|SmartSVN for Windows Version 7.0.1]&nbsp;&nbsp; {color:#ff0000}*\- NEW\!*{color}

\\
\\
\\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-Mac-7.0.1.tar|^smartsvn-macosx-7_0_1.tar.gz|SmartSVN Macintosh version 7.0.1]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}

\\
\\
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----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-Linux-7.0.1.tar.gz|^smartsvn-generic-7_0_1.tar.gz|SmartSVN Linux 7.0.1 tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}

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<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-6.6.9.zip|^smartsvn-windows-x86-setup-nojre-6_6_9.zip|SmartSVN for Windows Version 6.6.9]&nbsp;&nbsp; {color:#ff0000}*\- NEW\!*{color}

\\
\\
\\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-Mac-6.6..9tar|^smartsvn-macosx-6_6_9.tar.gz|SmartSVN Macintosh version 6.6.9]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}

\\
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\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-Linux-6.6.9.tar.gz|^smartsvn-generic-6_6_9.tar.gz|SmartSVN Linux Version 6.6.9]&nbsp;{color:#ff0000}*\- NEW\!*{color}

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<property name="body"><![CDATA[Here are some notes about the deployment of the Alfresco server at MBARI:

On November 7, 2007 Todd, Kent and Kevin had a teleconference with Joe Van De Graaff and Jared from Alfresco.  We had some questions about things and wanted to get a good feel for how Alfresco should be setup for the production environment.  Joe first talked about the current situation with Alfresco licensing and where Alfresco sits with their non-profit status.  Basically, Alfresco has changed from 50% discount to a 25% discount and they are not interested in name branding or references any more (more popular now).  There are basically two version of Alfresco: Community and Enterprise.  Community is the version we are using now and Enterprise is the only supported version.  So the bottom line is that if we want any kind of support, we have to install Enterprise and to install Enterprise, we need a support contract.  There is no way to install an unsupported Enterprise version.  We then turned the discussion to Jared to talk about the technical aspects.  I am not supremely confident that Jared has done any high visibility installations, so we may have to take a step of faith on some of his answers:

# *Do you have any general recommendations on server?* Yes, see [http://wiki.alfresco.com/wiki/Repository_Hardware].  In general it looks like their configuration pages have improved see [http://wiki.alfresco.com/wiki/Server_Configuration].
# *What database is best (knowing that we prefer SQL Server)?* He said SQL Server is one of the four main supported servers (MySQL, SQL Server, PostgreSQL, and Oracle).
# *Should the database be colocated with Alfresco install?* Should not matter unless you are going over REALLY long distances.  Even if you install in same machine as Alfresco, there is no way to do direct communication, it will still go over TCP/IP stack.
# *Why are we having problems with CIFS on Mac?* Hard to tell, but probably related to authenication.  We should use passthru (we are).  We asked about being on a LINUX box operating in a Windows Domain.  He thought that might be related and running it on a Windows box might help.
# *Does Alfresco support Kerberos authentication?* Yes.  I can verify that they have documentation and examples of Kerberos setup, but I have not tried it.  Todd was curious about this as this is where MBARI is probably going for single-sign-on authentication.
# *How do companies backup/restore Alfresco?* His feeling was that the big companies are using Alfresco's export mechanism.  This seems implausible to me as there is *huge* amount of overhead associated with exporting.  He said that you could export only the rules and backup the content through CIFS.  Again, this seems silly to me.  The view through CIFS is not the file system level view of the files.  Alfresco changes the files to manage them and then makes them look like native files when you view them through CIFS.  By backing up through CIFS, you would have to restore through the Alfresco server and I am not sure that is even really possible.  The export option seems better than that.  It sound to me like the best way to backup Alfresco is to have the file storage on a NetAppliance and coordinate database backups with the NetAppliance backups.  This would mean that if the server crashed, you could restore the filesystem and the DB to the correct state and point the new server to them.  This should work, but timing is key.  We could possibly have some Alfresco downtime when the backups occur, or just do the backups during a time when we feel like there would be little chance of changes occuring during backup.  Not really an optimal situation.
# *How does failover work?*  There are two options: cold and hot.  Hot is bascially clustering (you point both servers to the same DB and file location and the clustering keeps the local caches in synch), but then you have to pay for the CPU license for the hot backup machine.  The other option (cold) is to have an identically configured server sitting dark, bug configured exactly the same way as the production server.  This would allow you to make a DNS change and then fire up the cold server if you needed to do maintenance on the production server.  The cold option means you don't need a separate license.

So, I *think* the bottom line is that we will want to have a dedicated Alfresco server, 1 CPU (quad core would be nice and maybe buy a machine with two sockets in case we want to upgrade later).  Install Windows, point to a SQL Server instance that I.S. is maintaining, map a Tornado drive on the server and use that for the locale storage.  Have an identical server configured but sitting dark.  It will take some work, but setup a backup regime that will backup the NetAppliance share and the DB at the same time (this will need to be figured out).

]]></property>
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<property name="body"><![CDATA[Here are some notes about the deployment of the Alfresco server at MBARI:

On November 7, 2007 Todd, Kent and Kevin had a teleconference with Joe Van De Graaff and Jared from Alfresco.  We had some questions about things and wanted to get a good feel for how Alfresco should be setup for the production environment.  Joe first talked about the current situation with Alfresco licensing and where Alfresco sits with their non-profit status.  Basically, Alfresco has changed from 50% discount to a 25% discount and they are not interested in name branding or references any more (more popular now).  There are basically two version of Alfresco: Community and Enterprise.  Community is the version we are using now and Enterprise is the only supported version.  So the bottom line is that if we want any kind of support, we have to install Enterprise and to install Enterprise, we need a support contract.  There is no way to install an unsupported Enterprise version.  We then turned the discussion to Jared to talk about the technical aspects.  I am not supremely confident that Jared has done any high visibility installations, so we may have to take a step of faith on some of his answers:

# *Do you have any general recommendations on server?* Yes, see [http://wiki.alfresco.com/wiki/Repository_Hardware].  In general it looks like their configuration pages have improved see [http://wiki.alfresco.com/wiki/Server_Configuration].
# *What database is best (knowing that we prefer SQL Server)?* He said SQL Server is one of the four main supported servers (MySQL, SQL Server, PostgreSQL, and Oracle).
# *Should the database be colocated with Alfresco install?* Should not matter unless you are going over REALLY long distances.  Even if you install in same machine as Alfresco, there is no way to do direct communication, it will still go over TCP/IP stack.
# *Why are we having problems with CIFS on Mac?* Hard to tell, but probably related to authenication.  We should use passthru (we are).  We asked about being on a LINUX box operating in a Windows Domain.  He thought that might be related and running it on a Windows box might help.
# *Does Alfresco support Kerberos authentication?* Yes.  I can verify that they have documentation and examples of Kerberos setup, but I have not tried it.  Todd was curious about this as this is where MBARI is probably going for single-sign-on authentication.
# *How do companies backup/restore Alfresco?* His feeling was that the big companies are using Alfresco's export mechanism.  This seems implausible to me as there is *huge* amount of overhead associated with exporting.  He said that you could export only the rules and backup the content through CIFS.  Again, this seems silly to me.  The view through CIFS is not the file system level view of the files.  Alfresco changes the files to manage them and then makes them look like native files when you view them through CIFS.  By backing up through CIFS, you would have to restore through the Alfresco server and I am not sure that is even really possible.  The export option seems better than that.  It sound to me like the best way to backup Alfresco is to have the file storage on a NetAppliance and coordinate database backups with the NetAppliance backups.  This would mean that if the server crashed, you could restore the filesystem and the DB to the correct state and point the new server to them.  This should work, but timing is key.  We could possibly have some Alfresco downtime when the backups occur, or just do the backups during a time when we feel like there would be little chance of changes occuring during backup.  Not really an optimal situation.
# *How does failover work?*  There are two options: cold and hot.  Hot is bascially clustering (you point both servers to the same DB and file location and the clustering keeps the local caches in synch), but then you have to pay for the CPU license for the hot backup machine.  The other option (cold) is to have an identically configured server sitting dark, bug configured exactly the same way as the production server.  This would allow you to make a DNS change and then fire up the cold server if you needed to do maintenance on the production server.  The cold option means you don't need a separate license.

So]]></property>
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<property name="body"><![CDATA[Here are some notes about the deployment of the Alfresco server at MBARI:

On November 7, 2007 Todd, Kent and Kevin had a teleconference with Joe Van De Graaff and Jared from Alfresco.  We had some questions about things and wanted to get a good feel for how Alfresco should be setup for the production environment.  Joe first talked about the current situation with Alfresco licensing and where Alfresco sits with their non-profit status.  Basically, Alfresco has changed from 50% discount to a 25% discount and they are not interested in name branding or references any more (more popular now).  There are basically two version of Alfresco: Community and Enterprise.  Community is the version we are using now and Enterprise is the only supported version.  So the bottom line is that if we want any kind of support, we have to install Enterprise and to install Enterprise, we need a support contract.  There is no way to install an unsupported Enterprise version.  We then turned the discussion to Jared to talk about the technical aspects.  I am not supremely confident that Jared has done any high visibility installations, so we may have to take a step of faith on some of his answers:

# *Do you have any general recommendations on server?* Yes, see [http://wiki.alfresco.com/wiki/Repository_Hardware].  In general it looks like their configuration pages have improved see [http://wiki.alfresco.com/wiki/Server_Configuration].
# *What database is best (knowing that we prefer SQL Server)?* He said SQL Server is one of the four main supported servers (MySQL, SQL Server, PostgreSQL, and Oracle).
# *Should the database be colocated with Alfresco install?* Should not matter unless you are going over REALLY long distances.  Even if you install in same machine as Alfresco, there is no way to do direct communication, it will still go over TCP/IP stack.
# *Why are we having problems with CIFS on Mac?* Hard to tell, but probably related to authenication.  We should use passthru (we are).  We asked about being on a LINUX box operating in a Windows Domain.  He thought that might be related and running it on a Windows box might help.
# *Does Alfresco support Kerberos authentication?* Yes.  I can verify that they have documentation and examples of Kerberos setup, but I have not tried it.  Todd was curious about this as this is where MBARI is probably going for single-sign-on authentication.
# *How do companies backup/restore Alfresco?* His feeling was that the big companies are using Alfresco's export mechanism.  This seems implausible to me as there is *huge* amount of overhead associated with exporting.  He said that you could export only the rules and backup the content through CIFS.  Again, this seems silly to me.  The view through CIFS is not the file system level view of the files.  Alfresco changes the files to manage them and then makes them look like native files when you view them through CIFS.  By backing up through CIFS, you would have to restore through the Alfresco server and I am not sure that is even really possible.  The export option seems better than that.  It sound to me like the best way to backup Alfresco is to have the file storage on a NetAppliance and coordinate database backups with the NetAppliance backups.  This would mean that if the server crashed, you could restore the filesystem and the DB to the correct state and point the new server to them.  This should work, but timing is key.  We could possibly have some Alfresco downtime when the backups occur, or just do the backups during a time when we feel like there would be little chance of changes occuring during backup.  Not really an optimal situation.
# *How does failover work?*  There are two options: cold and hot.  Hot is bascially clustering (you point both servers to the same DB and file location and the clustering keeps the local caches in synch), but then you have to pay for the CPU license for the hot backup machine.  The other option (cold) is to have an identically configured server sitting dark, bug configured exactly the same way as the production server.  This would allow you to make a DNS change and then fire up the cold server if you needed to do maintenance on the production server.  The cold option means you don't need a separate license.

So, I *think* the bottom line is that we will want to have a dedicated Alfresco server, 1 CPU (quad core would be nice and maybe buy a machine with two sockets in case we want to upgrade later).  Install Windows, point to a SQL Server instance that I.S. is maintaining, map a Tornado drive on the server and use that for the locale storage.  Have an identical server configured but sitting dark.  It will take some work, but setup a backup regime that will backup the NetAppliance share and the DB at the same time (this will need to be figured out).

Here is a diagram of what this might look like:

!Alfresco Deployment.jpg|thumbnail!

If this is where we want to go, the cheapest way might be the following:

# Purchase a less potent server to use as the cold failover (maybe $4-5K)
# Purchase Gold SLA contract with Alfresco at 25% discount ($11,250)
# Configure cold server as alfresco.mbari.org, export content from oceana.shore.mbari.org and import to cold failover.
# See if engineering has a server that is not being utilized that we could put in the DMZ and migrate the Confluence and JIRA applications to that server (call this server oceana.shore.mbari.org.
# Reconfigure oceana.shore.mbari.org in the same way the cold failover was configured.  Point to the existing DB and file stores, bring down the cold failover, make a DNS switch to point to alfresco.mbari.org.  No export/import should be necessary.

So assuming we could find a server to host Confluence and JIRA, the bottom line cost would be around $15-16K with annual support contract of around $12K.  At some later time, we would probably want to purchase a test server and license (total of about $8,000, with an additional $2,800 annual contract for the test installation).]]></property>
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<property name="body"><![CDATA[Here are some notes about the deployment of the Alfresco server at MBARI:

On November 7, 2007 Todd, Kent and Kevin had a teleconference with Joe Van De Graaff and Jared from Alfresco.  We had some questions about things and wanted to get a good feel for how Alfresco should be setup for the production environment.  Joe first talked about the current situation with Alfresco licensing and where Alfresco sits with their non-profit status.  Basically, Alfresco has changed from 50% discount to a 25% discount and they are not interested in name branding or references any more (more popular now).  There are basically two version of Alfresco: Community and Enterprise.  Community is the version we are using now and Enterprise is the only supported version.  So the bottom line is that if we want any kind of support, we have to install Enterprise and to install Enterprise, we need a support contract.  There is no way to install an unsupported Enterprise version.  We then turned the discussion to Jared to talk about the technical aspects.  I am not supremely confident that Jared has done any high visibility installations, so we may have to take a step of faith on some of his answers:

# *Do you have any general recommendations on server?* Yes, see [http://wiki.alfresco.com/wiki/Repository_Hardware].  In general it looks like their configuration pages have improved see [http://wiki.alfresco.com/wiki/Server_Configuration].
# *What database is best (knowing that we prefer SQL Server)?* He said SQL Server is one of the four main supported servers (MySQL, SQL Server, PostgreSQL, and Oracle).
# *Should the database be colocated with Alfresco install?* Should not matter unless you are going over REALLY long distances.  Even if you install in same machine as Alfresco, there is no way to do direct communication, it will still go over TCP/IP stack.
# *Why are we having problems with CIFS on Mac?* Hard to tell, but probably related to authenication.  We should use passthru (we are).  We asked about being on a LINUX box operating in a Windows Domain.  He thought that might be related and running it on a Windows box might help.
# *Does Alfresco support Kerberos authentication?* Yes.  I can verify that they have documentation and examples of Kerberos setup, but I have not tried it.  Todd was curious about this as this is where MBARI is probably going for single-sign-on authentication.
# *How do companies backup/restore Alfresco?* His feeling was that the big companies are using Alfresco's export mechanism.  This seems implausible to me as there is *huge* amount of overhead associated with exporting.  He said that you could export only the rules and backup the content through CIFS.  Again, this seems silly to me.  The view through CIFS is not the file system level view of the files.  Alfresco changes the files to manage them and then makes them look like native files when you view them through CIFS.  By backing up through CIFS, you would have to restore through the Alfresco server and I am not sure that is even really possible.  The export option seems better than that.  It sound to me like the best way to backup Alfresco is to have the file storage on a NetAppliance and coordinate database backups with the NetAppliance backups.  This would mean that if the server crashed, you could restore the filesystem and the DB to the correct state and point the new server to them.  This should work, but timing is key.  We could possibly have some Alfresco downtime when the backups occur, or just do the backups during a time when we feel like there would be little chance of changes occuring during backup.  Not really an optimal situation.
# *How does failover work?*  There are two options: cold and hot.  Hot is bascially clustering (you point both servers to the same DB and file location and the clustering keeps the local caches in synch), but then you have to pay for the CPU license for the hot backup machine.  The other option (cold) is to have an identically configured server sitting dark, bug configured exactly the same way as the production server.  This would allow you to make a DNS change and then fire up the cold server if you needed to do maintenance on the production server.  The cold option means you don't need a separate license.

So, I *think* the bottom line is that we will want to have a dedicated Alfresco server, 1 CPU (quad core would be nice and maybe buy a machine with two sockets in case we want to upgrade later).  Install Windows, point to a SQL Server instance that I.S. is maintaining, map a Tornado drive on the server and use that for the locale storage.  Have an identical server configured but sitting dark.  It will take some work, but setup a backup regime that will backup the NetAppliance share and the DB at the same time (this will need to be figured out).

!Alfresco Deployment.jpg|thumbnail!
]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{note|title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{note}]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools

h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed. 

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool.  It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant.  You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory.

{note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above).  You can still use Together, but we are not eligible for upgrade/patches.
{note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

{warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN{code}{warning}

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{note}]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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h3. *SmartSVN GUI Installation Files*

* [SmartSVN-3.0.7.zip|^SmartSVN.zip][SmartSVN-3.0.4.zip|^SmartSVN_3.0.4.zip]
* [SmartSVN-3.0.4.zip|^SmartSVN.zip]\\]]></property>
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h3. *SmartSVN GUI Installation Files*

* [{color:#0000ff}SmartSVN-3.0.4.zip{color}|^SmartSVN_3.0.4.zip]
* [{color:#0000ff}SmartSVN-3.0.7.zip{color}|^SmartSVN-3_0_7.zip]\\]]></property>
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h3. *SmartSVN GUI Installation Files*

* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|^SmartSVN.zip]\\]]></property>
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h3. *SmartSVN GUI Installation Files*

* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip][|^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|^SmartSVN.zip]\\]]></property>
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h3. *SmartSVN GUI Installation Files*

* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip][|^SmartSVN.zip]
* [SmartSVN-3.0.4.zip|^SmartSVN.zip]\\]]></property>
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\\
&nbsp;

h3. *SmartSVN GUI Installation Files*

* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|^SmartSVN.zip]\\]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# ADCP: Acoustic Doppler Current Profiler -- a sonar that attempts to produce a record of water current velocities for a range of depths [http://en.wikipedia.org/wiki/Acoustic_Doppler_Current_Profiler] 
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AMQP: Advanced Message Queuing Protocol - [http://www.amqp.org]
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ARI-WG: Access to Remote Instrumentation in a distributed environment - Working Group. OpenGrid Forum [http://www.ogf.org/gf/group_info/view.php?group=ari-wg]
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# HDF: Hierarchical Data Format
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# JVM: Java Virtual Machine - http://en.wikipedia.org/wiki/Jvm
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MB/CA Current: a MBARI project in 2011
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# ODSS: Oceanographic Decision Support System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOI CI: Ocean Observatories Initiative CyberInfrastructure: [http://ci.oceanobservatories.org/] (Developers site: [http://ooici.net/])
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software).
# SCPI: Self Contained Plankton Imager, an MBARI project in 2011
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WCS: Web Coverage Service
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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Here's the standard method of adding a new directory to the subversion repository.]]></property>
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
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h3. *SmartSVN GUI Installation Files*


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h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-6.6.zip|^smartsvn-windows-x86-setup-nojre-6_6.zip|SmartSVN for Windows version 6.6]&nbsp;&nbsp; {color:#ff0000}*\- NEW\!*{color}

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h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-Mac-6.6.tar|^smartsvn-macosx-6_6.tar.gz|SmartSVN Macintosh version 6.6]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}

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h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-Linux-6.6.tar.gz|^smartsvn-generic-6_6.tar.gz|SmartSVN Linux version 6.6]&nbsp;{color:#ff0000}*\- NEW\!*{color}

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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
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h3. *SmartSVN GUI Installation Files*


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h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-6.6.zip|^smartsvn-windows-x86-setup-nojre-6_6.zip|SmartSVN for Windows version 6.6]&nbsp;&nbsp; {color:#ff0000}*\- NEW\!*{color}

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h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-Mac-6.6.tar|^smartsvn-macosx-6_6.tar.gz|SmartSVN Macintosh version 6.6]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}

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h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-Linux-6.6.tar.gz|^smartsvn-generic-6_6.tar.gz|SmartSVN Linux version 6.6]&nbsp;{color:#ff0000}*\- NEW\!*{color}

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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; _OR_

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).Step 4: Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.
           
1) Clicking on menu bar Modify - Commit Selection.
{code}
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; _OR{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}

{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}{color:#ff0000}{*}NOTE:*{color} {color:black}(Holding the shift key down allows the addition of more than one file at a time).{color}&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*.

_OR_

*2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).Step 4: Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.
           
1) Clicking on menu bar Modify - Commit Selection.
{code}
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; _OR{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}

{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}{color:#ff0000}{*}NOTE:*{color} {color:black}(Holding the shift key down allows the addition of more than one file at a time).{color}&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; OR_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).Step 4: Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.
           
1) Clicking on menu bar Modify - Commit Selection.
{code}
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; _OR{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}

{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}{color:#ff0000}{*}NOTE:*{color} {color:black}(Holding the shift key down allows the addition of more than one file at a time).{color}&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_OR_
*2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).Step 4: Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.
           
1) Clicking on menu bar Modify - Commit Selection.
{code}
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; _OR{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}

{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}{color:#ff0000}{*}NOTE:*{color} {color:black}(Holding the shift key down allows the addition of more than one file at a time).{color}&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).Step 4: Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.
           
1) Clicking on menu bar Modify - Commit Selection.
{code}
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; _OR{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}

{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}{color:#ff0000}{*}NOTE:*{color} {color:black}(Holding the shift key down allows the addition of more than one file at a time).{color}&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

To add a new file to a directory, follow these steps:Step 1: You must first have a working copy of the directory (See item # 7).Step 2: Create the new file(s) inside your checked-out working copy of the directory.Step 3: In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added. Click the new file(s) with your mouse and add the file(s) by either:&nbsp;1) Clicking on menu bar *Modify - Add Selection*. If the file contains binary dataclick *Modify - Add Selection Binary*. OR2) Clicking on the user interface button (white rectangle with a red "plus" sign onit). If the file is a binary, click the binary add button which is white with a red"plus" sign and 01 on it.NOTE: (Holding the shift key down allows the addition of more than one file at a time).Step 4: Commit the selection. This step actually "Adds" (checks-in) the file(s) to therepository. This can either be done with the file menu or with the user interfacebutton.1) Clicking on menu bar *Modify - Commit Selection*. OR{color:black}{*}2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color}{color:black}left on it).{color}{color:black}{*}NOTE:*{color} {color:black}(Holding the shift key down allows the addition of more than one file at a time).{color}{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color}{color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color}{color:black}are not recursive.{color}
\\
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; _OR_

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; {color:#ff0000}{*}NOTE:*{color} (Holding the shift key down allows the addition of more than one file at a time).*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; _OR{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}{color:#ff0000}{*}NOTE:*{color} {color:black}(Holding the shift key down allows the addition of more than one file at a time).{color}&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; _OR_

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).Step 4: Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.
            1) Clicking on menu bar Modify - Commit Selection.
{code}
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; _OR{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}

{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}{color:#ff0000}{*}NOTE:*{color} {color:black}(Holding the shift key down allows the addition of more than one file at a time).{color}&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}

{code}
{color:#ff0000}{*}NOTE:*{color} {color:black}(Holding the shift key down allows the addition of more than one file at a time).{color}
{code}

{code}&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
&nbsp;
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}

{code}
{color:#ff0000}{*}NOTE:*{color} {color:black}(Holding the shift key down allows the addition of more than one file at a time).{color}
{code}

{code}

&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
&nbsp;
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}

{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}

&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
&nbsp;
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
&nbsp;
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
&nbsp;
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}

Step 4: Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.
           
1) Clicking on menu bar Modify - Commit Selection.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; _OR{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}

{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}{color:#ff0000}{*}NOTE:*{color} {color:black}(Holding the shift key down allows the addition of more than one file at a time).{color}&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1) Clicking on menu bar Modify - Commit Selection.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; _OR{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}

{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}{color:#ff0000}{*}NOTE:*{color} {color:black}(Holding the shift key down allows the addition of more than one file at a time).{color}&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1) Clicking on menu bar Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; _OR{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}

{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}{color:#ff0000}{*}NOTE:*{color} {color:black}(Holding the shift key down allows the addition of more than one file at a time).{color}&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}

{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}{color:#ff0000}{*}NOTE:*{color} {color:black}(Holding the shift key down allows the addition of more than one file at a time).{color}&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of adding a new directory to the subversion repository.
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._

To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}{color:#ff0000}
{code}{*}NOTE:*{color} {color:black}(Holding the shift key down allows the addition of more than one file at a time).
{code}{color}&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; http://www.cenic.org/
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
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\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
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{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
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{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
&nbsp; \\ {color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}{color:blue}Step 1:{color} {color:black}Make sure that you have not made any uncommitted modifications to the file.{color} {color:black}This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was immediately before you deleted it.{color}{color:blue}Step 2:{color} {color:black}Remove the file from your working copy of the directory. This can done by first{color} {color:black}highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color}{color:blue}Step3:{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first{color} {color:black}highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}{color:blue}Step 4:{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}
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{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}. NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color} \\

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color} \\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}http://www.cvshome.org/{color} {color:black}and download the CVS manual.{color}
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<property name="body"><![CDATA[h2.


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h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; {color:#ff0033}{*}NOTE:*{color} {color:#ff0033}In the rare event the administrator is on vacation or unavailable, please&nbsp;submit your CVS request to the IS Remedy page at:&nbsp;{color} [https://ishelp.shore.mbari.org/helpdesk/WebObjects/Helpdesk] {color:#ff0033}and it will be assigned by IS appropriately based on urgency level.{color}

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;CVS command Line Reference. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/.&nbsp];

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

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[Welcome to CVS\!|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

[CVS Graphical User Interface (GUI) Client Software Downloads|CLT:CVS Client Software Downloads] \- {color:#3300cc}Windows, Mac, Linux Systems{color}

[Setting up&nbsp;the WinCVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]

[Adding code to CVS Repository with WinCVS GUI|CLT:Adding code to CVS Repository with WinCVS GUI]

[Command Line Access to CVS Repository&nbsp;(i.e., no GUI)|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)] *\-* {color:#3300cc}For Linux System Users{color}

[View the CVS Repository|http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/ ]\\
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h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at http://subversion.tigris.org/. Excellent documentation on using Subversion can be found at http://svnbook.red-bean.com/

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;http://kahuna.shore.mbari.org/viewvc/?root=svn.

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[SVN Client Software Downloads|CLT:SVN Client Software Downloads] {color:#ff0000}\- Windows, Macs, Linux Systems{color}

[Setting up SVN Client&nbsp;to MBARI SVN Repository|CLT:Setting up SmartSVN]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository]

[View the SVN Repository|http://kahuna.shore.mbari.org/viewvc/?root=svn]

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<property name="body"><![CDATA[h2.


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h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;CVS command Line Reference. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at http://cvsgui.sourceforge.net/.&nbsp; Detailed documentation on using CVS can be found at http://ximbiot.com/cvs/manual/.&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/.

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[Welcome to CVS\!|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

[CVS Graphical User Interface (GUI) Client Software Downloads|CLT:CVS Client Software Downloads] \- {color:#3300cc}Windows, Mac, Linux Systems{color}

[Setting up&nbsp;the WinCVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]

[Adding code to CVS Repository with WinCVS GUI|CLT:Adding code to CVS Repository with WinCVS GUI]

[Command Line Access to CVS Repository&nbsp;(i.e., no GUI)|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)] *\-* {color:#3300cc}For Linux System Users{color}

[View the CVS Repository|http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/ ]\\
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[Welcome to CVS\!|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

[CVS Graphical User Interface (GUI) Client Software Downloads|CLT:CVS Client Software Downloads] \- {color:#3300cc}Windows, Mac, Linux Systems{color}

[Setting up&nbsp;the WinCVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]

[Adding code to CVS Repository with WinCVS GUI|CLT:Adding code to CVS Repository with WinCVS GUI]

[Command Line Access to CVS Repository&nbsp;(i.e., no GUI)|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)] *\-* {color:#3300cc}For Linux System Users{color}

[View the CVS Repository|http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/ ]\\
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[SVN Client Software Downloads|CLT:SVN Client Software Downloads] {color:#ff0000}\- Windows, Macs, Linux Systems{color}

[Setting up SVN Client&nbsp;to MBARI SVN Repository|CLT:Setting up SmartSVN]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository]

[View the SVN Repository|http://kahuna.shore.mbari.org/viewvc/?root=svn]

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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - http://www.epa.gov/
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.

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h3. *SmartSVN GUI Installation Files*


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h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip] {color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]\\
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h3. Macintosh

* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]&nbsp; ({color:#ff0000}Mac&nbsp;OS X, version 10.4 or higher{color})
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h3. Linux

* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp; ({color:#ff0000}Note: Requires JRE 1.4.1 or higher{color})
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h3. *SmartSVN GUI Installation Files*


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h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip] {color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]\\
\\

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h3. Macintosh

* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]&nbsp; ({color:#ff0000}Mac&nbsp;OS X, version 10.4 or higher{color})
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h3. Linux

* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp; ({color:#ff0000}Note: Requires JRE 1.4.1 or higher{color})
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h3. *SmartSVN GUI Installation Files*


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h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip] {color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]\\
\\

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h3. Macintosh

* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]&nbsp; ({color:#ff0000}Mac&nbsp;OS X, version 10.4 or higher{color})
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h3. Linux

* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp; ({color:#ff0000}Note: Requires JRE 1.4.1 or higher{color})
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There are&nbsp;two recommended CVS Clients to access the MBARI CVS Respository including:&nbsp;{color:#ff0000}{*}WinCVS{*}{color} and {color:#ff0000}{*}SmartCVS{*}{color}.&nbsp;&nbsp; Both clients work for all major operating systems including Windows, Macintosh, and Linux systems.&nbsp;The key bits of information to use when setting up either client are the following:
* User&nbsp; (Your MBARI user/e-mail&nbsp;account, e.g., _salamy_)
* Repository Server (MBARI CVS Repository is hosted on *{_}moonjelly{_}*)
* CVSROOT (*_/home/cvs{_}*)

Thus, the full CVSROOT path for user _salamy_ would be:&nbsp;&nbsp;&nbsp; salamy@moonjelly:/home/cvs&nbsp;

----
\\

h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


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h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS Getting-Started Tutorial|^smartcvs-tutorial.pdf] \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

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h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

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There are&nbsp;two recommended CVS Clients to access the MBARI CVS Respository including:&nbsp;WinCVS and SmartCVS.&nbsp;&nbsp; Both clients work for all major operating systems including Windows, Macintosh, and Linux systems.&nbsp;The key bits of information to use when setting up either client are the following:
* User&nbsp; (Your MBARI user/e-mail&nbsp;account, e.g., _salamy_)
* Repository Server (MBARI CVS Repository is hosted on *{_}moonjelly{_}*)
* CVSROOT (*_/home/cvs{_}*)

Thus, the full CVSROOT path for user _salamy_ would be:&nbsp;&nbsp;&nbsp; salamy@moonjelly:/home/cvs&nbsp;

----
&nbsp;
\\

h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS Getting-Started Tutorial|^smartcvs-tutorial.pdf] \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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<property name="body"><![CDATA[There are&nbsp;two recommended CVS Clients to access the MBARI CVS Respository including:&nbsp;WinCVS and SmartCVS.&nbsp;&nbsp; Both clients work for all major operating systems including Windows, Macintosh, and Linux systems.&nbsp;The key bits of information to use when setting up either client are the following:
* User&nbsp; (Your MBARI user/e-mail&nbsp;account, e.g., _salamy_)
* Repository Server (MBARI CVS Repository is hosted on *{_}moonjelly{_}*)
* CVSROOT (*_/home/cvs{_}*)

Thus, the full CVSROOT path for user _salamy_ would be:&nbsp;&nbsp;&nbsp; salamy@moonjelly:/home/cvs&nbsp;

\\
&nbsp;

h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS Getting-Started Tutorial|^smartcvs-tutorial.pdf] \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS Getting-Started Tutorial|^smartcvs-tutorial.pdf] \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-6.5.5.zip|^smartsvn-windows-x86-setup-nojre-6_5_5.zip|SmartSVN for Windows version 6.5.5]&nbsp;&nbsp; {color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]\\
\\
\\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.9.tar.gz|^smartsvn-macosx-4_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.9.tar.gz|^smartsvn-generic-4_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]\\
\\ \\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.9.tar.gz|^smartsvn-macosx-4_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.9.tar.gz|^smartsvn-generic-4_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
\\
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There are&nbsp;two recommended CVS Clients to access the MBARI CVS Respository including:&nbsp;{color:#ff0000}{*}WinCVS{*}{color} and {color:#ff0000}{*}SmartCVS{*}{color}.&nbsp;&nbsp; Both clients work for all major operating systems including Windows, Macintosh, and Linux systems.&nbsp;The key bits of information to use when setting up either client are the following:
* {color:#0000cc}Your access method needs to be set to&nbsp;{color}{color:#0000cc}{*}pserver{*}{color}{color:#0000cc}&nbsp;(SmartCVS) or{color} {color:#0000cc}{*}passwd file on server{*}{color} {color:#0000cc}(WinCVS){color}
* {color:#0000cc}User&nbsp; (Your MBARI user/e-mail&nbsp;account, e.g.,{color} {color:#0000cc}{_}salamy{_}{color}{color:#0000cc}){color}
* {color:#0000cc}Repository Server (MBARI CVS Repository is hosted on{color} {color:#0000cc}{*}{_}moonjelly{_}{*}{color}{color:#0000cc}){color}
* {color:#0000cc}CVSROOT ({color}{color:#0000cc}{*}_/home/cvs{_}{*}{color}{color:#0000cc}){color}

Thus, the full CVSROOT path for user _salamy_ would be:&nbsp;&nbsp;&nbsp; salamy@moonjelly:/home/cvs&nbsp;

----
\\

h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-7.1.zip|^smartcvs-win32-setup-nojre-7_1.zip|SmartCVS Windows version 7.1] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOSX-7.1.tar.gz|^smartcvs-macosx-7_1.tar.gz|SmartCVS Macintosh Version 7.1] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartSVN-Linux-7.1.tar.gz|^smartcvs-generic-7_1.tar.gz|SmartSVN Linux Version 7.1] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}({color}{color:#0066cc}{*}NOTE:*{color}{color:#0066cc}&nbsp;Setup same for MacCVS and gCVS as well){color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS Getting-Started Tutorial|^smartcvs-tutorial.pdf] \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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There are&nbsp;two recommended CVS Clients to access the MBARI CVS Respository including:&nbsp;{color:#ff0000}{*}WinCVS{*}{color} and {color:#ff0000}{*}SmartCVS{*}{color}.&nbsp;&nbsp; Both clients work for all major operating systems including Windows, Macintosh, and Linux systems.&nbsp;The key bits of information to use when setting up either client are the following:
* {color:#0000cc}Your access method needs to be set to&nbsp;{color}{color:#0000cc}{*}pserver{*}{color}{color:#0000cc}&nbsp;(SmartCVS) or{color} {color:#0000cc}{*}passwd file on server{*}{color} {color:#0000cc}(WinCVS){color}
* {color:#0000cc}User&nbsp; (Your MBARI user/e-mail&nbsp;account, e.g.,{color} {color:#0000cc}{_}salamy{_}{color}{color:#0000cc}){color}
* {color:#0000cc}Repository Server (MBARI CVS Repository is hosted on{color} {color:#0000cc}{*}{_}moonjelly{_}{*}{color}{color:#0000cc}){color}
* {color:#0000cc}CVSROOT ({color}{color:#0000cc}{*}_/home/cvs{_}{*}{color}{color:#0000cc}){color}

Thus, the full CVSROOT path for user _salamy_ would be:&nbsp;&nbsp;&nbsp; salamy@moonjelly:/home/cvs&nbsp;

----
\\

h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-7.0.2.zip|^smartcvs-win32-setup-nojre-7_0_2.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-7.0.2.tar.gz|^smartcvs-macosx-7_0_2.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-7.0.2.tar.gz|^smartcvs-generic-7_0_2.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}({color}{color:#0066cc}{*}NOTE:*{color}{color:#0066cc}&nbsp;Setup same for MacCVS and gCVS as well){color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS Getting-Started Tutorial|^smartcvs-tutorial.pdf] \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4. &nbsp;


h3. CVS Client Set-Up Instructions

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. &nbsp;


h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* SmartCVS-MacOS-6.0.8.tar.gz *\-* {color:#0066cc}{*}Macintosh{*}{color}
* SmartCVS-Linux-6.0.8.tar.gz *\-* {color:#0066cc}{*}Linux{*}{color}

h4. &nbsp;


h3. CVS Client Set-Up Instructions

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. &nbsp;


h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4. &nbsp;


h3. CVS Client Set-Up Instructions

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. &nbsp;


h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.

----


h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h4. {color:#ff0000}SmartCVS{color}

* {color:#000000}[{color:#000000}SmartCVS Getting Started Tutorial (PDF document){color}|^smartcvs-tutorial.pdf]{color}\\

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h4. {color:#ff0000}SmartCVS{color}

* {color:#000000}\[{color}{color:#000000}SmartCVS Getting Started Tutorial (PDF document){color}\|^smartcvs-tutorial.pdf\]\\ \\

----\\ \\

h3. CVS Administrative Information

\* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- NOTE: Password Access Required

\\
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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. {color:#ff0000}SmartCVS{color}

* SmartCVS-Win32-6.0.8.zip *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* SmartCVS-MacOS-6.0.8.tar.gz *\-* {color:#0066cc}{*}Macintosh{*}{color}
* SmartCVS-Linux-6.0.8.tar.gz *\-* {color:#0066cc}{*}Linux{*}{color}

h4. &nbsp;


h3. CVS Client Set-Up Instructions

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. &nbsp;


h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. {color:#ff0000}SmartCVS{color}

* SmartCVS-Win32-6.0.8.zip *\-* {color:#0066cc}{*}Windows (Requires{*}{color}
* SmartCVS-MacOS-6.0.8.tar.gz
* SmartCVS-Linux-6.0.8.tar.gz

h4. &nbsp;


h3. CVS Client Set-Up Instructions

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. &nbsp;


h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modeling with UML (JBuilder 2008 Enterprise)

You can download JBuilder 2008 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded and installed, you need to copy the following [.slip|https://alfresco.mbari.org/alfresco/webdav/Engineering/Tools/Collaboration%20Tools/CodeGear%20JBuilder/concurrent_31474.slip] file to the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* {color:#000000}\[{color}{color:#000000}SmartCVS Getting Started Tutorial (PDF document){color}\|^smartcvs-tutorial.pdf\]
\\

\---\-
\\
\\
\\
\\

h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* {color:#000000}\[{color}{color:#000000}SmartCVS Getting Started Tutorial (PDF document){color}\|^smartcvs-tutorial.pdf\] \\

h4.


----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* {color:#000000}SmartCVS Getting Started Tutorial (PDF document){color}

h4.


----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* {color:#000000}[{color:#000000}SmartCVS Getting Started Tutorial{color}|^smartcvs-tutorial.pdf]{color} {color:#000000}*\-*{color} {color:#0066cc}{*}PDF Document{*}{color}

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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<property name="body"><![CDATA[h3. Introduction
This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to pages with details about each specific tool.

* Content Management Tool (Alfresco)
* WIKI Collaboration Pages (Confluence)
* Issue (bug) tracking (JIRA)
* UML (?)

Here are some links to pages describing the various tools available and information about why we chose the ones we chose.  

* Content Management Tools
* WIKI Tools
* Issue Bug Trackers
* UML
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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* SmartCVS Getting-Started Tutorial \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by http://www.seadatanet.org/
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h4. {color:#ff0000}SmartCVS{color}

* {color:#000000}\[{color}{color:#000000}SmartCVS Getting Started Tutorial (PDF document){color}\|^smartcvs-tutorial.pdf\]\\ \\

----\\ \\

h3. CVS Administrative Information

\* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- NOTE: Password Access Required

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----
\\
&nbsp;

[SVN Client Software Downloads|CLT:SVN Client Software Downloads] {color:#ff0000}\- Windows, Macs, Linux Systems{color}

[Setting up SmartSVN to MBARI SVN Repository|CLT:Setting up SmartSVN][Setting up SmartSVN|CLT:Setting up SmartSVN]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository]

[View the SVN Repository|http://kahuna.shore.mbari.org/viewvc/?root=svn]

\\
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by http://www.seadatanet.org/
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* {color:#000000}\[{color}{color:#000000}SmartCVS Getting Started Tutorial (PDF document){color}\|^smartcvs-tutorial.pdf\]\\

----\\ \\

&nbsp;CVS Administrative Information
* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
&nbsp;]]></property>
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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* {color:#000000}\[{color}{color:#000000}SmartCVS Getting Started Tutorial (PDF document){color}\|^smartcvs-tutorial.pdf\]\\

----\\ \\ \\ \\ \\ \\ \\ \\ \\

CVS Administrative Information
* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
&nbsp;]]></property>
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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* {color:#000000}\[{color}{color:#000000}SmartCVS Getting Started Tutorial (PDF document){color}\|^smartcvs-tutorial.pdf\]
\\ \\ \\ \\

----\\
\\
\\
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\\ CVS Administrative Information
* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* {color:#000000}\[{color}{color:#000000}SmartCVS Getting Started Tutorial (PDF document){color}\|^smartcvs-tutorial.pdf\]
* &nbsp;\\

----\\ \\ \\

CVS Administrative Information
* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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----
\\
&nbsp;

[SVN Client Software Downloads|CLT:SVN Client Software Downloads] {color:#ff0000}\- Windows, Macs, Linux Systems{color}

[Setting up SmartSVN to MBARI SVN Repository|CLT:Setting up SmartSVN]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository]

[View the SVN Repository|http://kahuna.shore.mbari.org/viewvc/?root=svn]

\\
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h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* {color:#000000}\[{color}{color:#000000}SmartCVS Getting Started Tutorial (PDF document){color}\|^smartcvs-tutorial.pdf\]\\

----\\ \\ \\ \\

CVS Administrative Information
* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
&nbsp;]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)| | | | | | | | |Not a very professional install.| |
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | | |
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | | | | | |
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]| | | | | | | | | | | | |$2000 (we get a 10% discount)|
]]></property>
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----
\\
&nbsp;

[SVN Client Software Downloads|CLT:SVN Client Software Downloads] {color:#ff0000}\- Windows, Macs, Linux Systems{color}

[Setting up SmartSVN to MBARI SVN Repository|CLT:Setting up SmartSVN][|CLT:Setting up a SVN Graphical User Interface (GUI)]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository]

\\
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Artisan Studio|http://www.artisansw.com/products]|X| | | | | | | | | | |Not a very professional install.| |
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | | |
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | | | | | |
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]| | | | | | | | | | | | |$2000 (we get a 10% discount)|
]]></property>
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----
\\
&nbsp;

[SVN Client Software Downloads|CLT:SVN Client Software Downloads] {color:#ff0000}\- Windows, Macs, Linux Systems{color}

[Setting up SmartSVN to MBARI SVN Repository|CLT:Setting up SmartSVN][|CLT:Setting up SmartSVN]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository]

\\
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\\
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Artisan Studio|http://www.artisansw.com/products]|{centertext}(/){centertext}|(x)|(x)| | | | | | | | |Not a very professional install.| |
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | | |
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | | | | | |
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]| | | | | | | | | | | | |$2000 (we get a 10% discount)|
]]></property>
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<property name="body"><![CDATA[Nice that you can add custom stencils for using your own custom elements in a model.]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)| | | | | | | | |Not a very professional install.| |
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | | |
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | | | | | |
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]| | | | | | | | | | | | |$2000 (we get a 10% discount)|
]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)| | | | | | | | |Not a very professional install.| |
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | | |
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | | | | | |
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)| | | | | | |$2000 (we get a 10% discount)|
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<property name="body"><![CDATA[My initial impression of the product is pretty poor.  The installation was not very professional at all.  The install requirements were very picky and if you had a PATH environment variable longer than 1000 characters (most people probably do), the installation would crash.  Getting a license was very slow and their support seems like a pretty small, rag-tag bunch.]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* Artisan Studio
* Borland's Together
* IBM Rational Software Architect
* Oracle JDeveloper
* MagicDraw
* Omondo
* VisualParadigm

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Artisan Studio|http://www.artisansw.com/products]| | | | | | | | | | | | | |
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | | |
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | | |
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | | | | | |
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]| | | | | | | | | | | | |$2000 (we get a 10% discount)|
]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|Artisan Studio| | | | | | | | | | | | | |
|Borland Together| | | | | | | | | | | | | |
|Embedded Plus| | | | | | | | | | | | | |
|IBM Rational Software Architect| | | | | | | | | | | | | |
|JDeveloper| | | | | | | | | | | | | |
|MagicDraw| | | | | | | | | | | | | |
|Omondo| | | | | | | | | | | | | |
|PragmaDev| | | | | | | | | | | | | |
|Rhapsody| | | | | | | | | | | | | |
|Sparx| | | | | | | | | | | | | |
|Umbrello| | | | | | | | | | | | | |
|VisualParadigm| | | | | | | | | | | | | |
|Posiedon| | | | | | | | | | | | | |
]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Artisan Studio|http://www.artisansw.com/products]|X| | | | | | | | | | | | |
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | | |
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | | | | | |
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]| | | | | | | | | | | | |$2000 (we get a 10% discount)|
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Artisan Studio|http://www.artisansw.com/products]| | | | | | | | | | | | | |
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | | |
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | | | | | |
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]| | | | | | | | | | | | |$2000 (we get a 10% discount)|
]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Artisan Studio|http://www.artisansw.com/products]|X| | | | | | | | | | |Not a very projessional install.| |
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | | |
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | | | | | |
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]| | | | | | | | | | | | |$2000 (we get a 10% discount)|
]]></property>
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<property name="body"><![CDATA[h2. Adding your code to MBARI's SVN repository

Here's the standard method of adding a new directory to the subversion repository.

1) On your local machine create the following directory structure
{noformat}
tempdir
`~~ myproject       <-- Replace 'myproject' with the name of your project
   `~~ tags
   `~~ branches
   `~~ trunk
      `~~ agent
      `~~ ctd2007
{noformat}
2) cd to _tempdir_ and run the following command
{{svn import myproject svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject}}

3) To check out _myproject's_ main trunk on another machine you run the command
{{svn co svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject/trunk myproject{}}}{note:title=Be Careful}
Notice that we've added '/trunk' to the SVN URL above to check out only the trunk (main development line). If you omit '/trunk' you will check out all tags and branches as well as the trunk.{note}
A free on-line guide to SVN is available at [http://svnbook.red-bean.com/]. The most useful svn commands are
{noformat}
svn status                            <-- shows you the status of files in your project
svn add some/new/file                 <-- add a new file to version control
svn del some/old/file                 <-- remove a file from version control
svn update                            <-- Get changes from the repository
svn commit -m "some commit message"   <-- commit changes to the repository
svn help
{noformat}
If you find that you can't connect to the svn repository contact Karen Salamy. She may need to give you access permissions.]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | | |
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | | | | | |
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. I did hit what might be a show stopper. Associations did not generate code! Awaiting techincal support.|$2000 (we get a 10% discount)|
]]></property>
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<property name="body"><![CDATA[\\

h3. *CVS Client&nbsp;Installation Files*

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}

h3. &nbsp;


h3. CVS Client Set-Up Instructions

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. &nbsp;


h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
&nbsp;]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | |$4000|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | | | | | |
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. I did hit what might be a show stopper. Associations did not generate code! Awaiting techincal support.|$2000 (we get a 10% discount)|
]]></property>
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<property name="body"><![CDATA[h2.

----
\\ \\

Adding your code to MBARI's SVN Source Code Repository

SVN Client Software Downloads

Setting up SmartSVN to MBARI SVN Repository\\ \\ \\ \\
h2. Adding your code to MBARI's SVN repository

Here's the standard method of adding a new directory to the subversion repository.

1) On your local machine create the following directory structure
{noformat}
tempdir
`~~ myproject       <-- Replace 'myproject' with the name of your project
   `~~ tags
   `~~ branches
   `~~ trunk
      `~~ agent
      `~~ ctd2007
{noformat}
2) cd to _tempdir_ and run the following command
{{svn import myproject svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject}}

3) To check out _myproject's_ main trunk on another machine you run the command
{{svn co svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject/trunk myproject}} {note:title=Be Careful}
Notice that we've added '/trunk' to the SVN URL above to check out only the trunk (main development line). If you omit '/trunk' you will check out all tags and branches as well as the trunk. {note}
A free on-line guide to SVN is available at [http://svnbook.red-bean.com/]. The most useful svn commands are
\\
{noformat}
svn status                            <-- shows you the status of files in your project
svn add some/new/file                 <-- add a new file to version control
svn del some/old/file                 <-- remove a file from version control
svn update                            <-- Get changes from the repository
svn commit -m "some commit message"   <-- commit changes to the repository
svn help
{noformat}
If you find that you can't connect to the svn repository contact Karen Salamy. She may need to give you access permissions.]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | | | | | |Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | |$4000|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | | | | |Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. I did hit what might be a show stopper. Associations did not generate code! Awaiting techincal support.|$2000 (we get a 10% discount)|
]]></property>
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<property name="body"><![CDATA[----
h2. Adding your code

Here's the standard method of adding a new directory to the subversion repository.

1) On your local machine create the following directory structure
{noformat}
tempdir
`~~ myproject       <-- Replace 'myproject' with the name of your project
   `~~ tags
   `~~ branches
   `~~ trunk
      `~~ agent
      `~~ ctd2007
{noformat}
2) cd to _tempdir_ and run the following command
{{svn import myproject svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject}}

3) To check out _myproject's_ main trunk on another machine you run the command
{{svn co svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject/trunk myproject}} {note:title=Be Careful}


Notice that we've added '/trunk' to the SVN URL above to check out only the trunk (main development line). If you omit '/trunk' you will check out all tags and branches as well as the trunk. {note}\\

A free on-line guide to SVN is available at [http://svnbook.red-bean.com/]. The most useful svn commands are
\\
{noformat}
svn status                            <-- shows you the status of files in your project
svn add some/new/file                 <-- add a new file to version control
svn del some/old/file                 <-- remove a file from version control
svn update                            <-- Get changes from the repository
svn commit -m "some commit message"   <-- commit changes to the repository
svn help
{noformat}
If you find that you can't connect to the svn repository contact Karen Salamy. She may need to give you access permissions.]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | | | | |Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | |$4000|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | | | | |Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. I did hit what might be a show stopper. Associations did not generate code! Awaiting techincal support.|$2000 (we get a 10% discount)|
]]></property>
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----
\\
&nbsp;

[SVN Client Software Downloads|CLT:SVN Client Software Downloads]

[Setting up SmartSVN to MBARI SVN Repository|CLT:Setting up a SVN Graphical User Interface (GUI)]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository]

\\
\\
\\
\\
&nbsp;

h2. Adding your code to MBARI's SVN repository

Here's the standard method of adding a new directory to the subversion repository.

1) On your local machine create the following directory structure
{noformat}
tempdir
`~~ myproject       <-- Replace 'myproject' with the name of your project
   `~~ tags
   `~~ branches
   `~~ trunk
      `~~ agent
      `~~ ctd2007
{noformat}
2) cd to _tempdir_ and run the following command
{{svn import myproject svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject}}

3) To check out _myproject's_ main trunk on another machine you run the command
{{svn co svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject/trunk myproject}} {note:title=Be Careful}
Notice that we've added '/trunk' to the SVN URL above to check out only the trunk (main development line). If you omit '/trunk' you will check out all tags and branches as well as the trunk. {note}
A free on-line guide to SVN is available at [http://svnbook.red-bean.com/]. The most useful svn commands are
\\
\\
{noformat}
svn status                            <-- shows you the status of files in your project
svn add some/new/file                 <-- add a new file to version control
svn del some/old/file                 <-- remove a file from version control
svn update                            <-- Get changes from the repository
svn commit -m "some commit message"   <-- commit changes to the repository
svn help
{noformat}
If you find that you can't connect to the svn repository contact Karen Salamy. She may need to give you access permissions.]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | | |Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | |$4000|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | |Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET| |Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. I did hit what might be a show stopper. Associations did not generate code! Awaiting techincal support.|$2000 (we get a 10% discount)|
]]></property>
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h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip] {color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]\\
\\

----
h3. Macintosh

* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]&nbsp; ({color:#ff0000}Mac&nbsp;OS X, version 10.4 or higher{color})
\\
\\
\\

----
h3. Linux

* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp; ({color:#ff0000}Note: Requires JRE 1.4.1 or higher{color})]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | |$4000|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET| |Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. I did hit what might be a show stopper. Associations did not generate code! Awaiting techincal support.|$2000 (we get a 10% discount)|
]]></property>
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<property name="body"><![CDATA[----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip] {color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]\\
\\

----
h3. Macintosh

* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]&nbsp; ({color:#ff0000}Mac&nbsp;OS X, version 10.4 or higher{color})
\\
\\
\\

----
h3. Linux

* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp; ({color:#ff0000}Note: Requires JRE 1.4.1 or higher{color})\\ \\ \\]]></property>
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<id name="id">129</id>
<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | |$4000|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. I did hit what might be a show stopper. Associations did not generate code! Awaiting techincal support.|$2000 (we get a 10% discount)|
]]></property>
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<id name="id">130</id>
<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | |After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear!|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | |$4000|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. I did hit what might be a show stopper. Associations did not generate code! Awaiting techincal support.|$2000 (we get a 10% discount)|
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[SVN Client Software Downloads|CLT:SVN Client Software Downloads]

[Setting up SmartSVN to MBARI SVN Repository|CLT:Setting up a SVN Graphical User Interface (GUI)]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository]

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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | | |
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | | | | | |
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)| | | | | | |$2000 (we get a 10% discount)|
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | | |
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | | | | | |
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)| | | | | | |$2000 (we get a 10% discount)|
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[SVN Client Software Downloads|CLT:SVN Client Software Downloads] {color:#ff0000}\- Windows, Macs, Linux Systems{color}

[Setting up SmartSVN to MBARI SVN Repository|CLT:Setting up a SVN Graphical User Interface (GUI)]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository]

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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | | |
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | | | | | |
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)| |Eclipse, NetBeans, InteliJ, JDeveloper| | | |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great.|$2000 (we get a 10% discount)|
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[SVN Client Software Downloads|CLT:SVN Client Software Downloads] {color:#ff0000}\- Windows, Macs, Linux Systems{color}

[Setting up SmartSVN to MBARI SVN Repository|CLT:Setting up a SVN Graphical User Interface (GUI)][|CLT:Setting up a SVN Graphical User Interface (GUI)]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository]

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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | | |
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | | | | | |
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out.|$2000 (we get a 10% discount)|
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | | |$3000 (this has a back support penalty, normally $1500)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | | |
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | | | | | | |
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. I did hit what might be a show stopper. Associations did not generate code! Awaiting techincal support.|$2000 (we get a 10% discount)|
]]></property>
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----
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[SVN Client Software Downloads|CLT:SVN Client Software Downloads] {color:#ff0000}\- Windows, Macs, Linux Systems{color}

[Setting up SmartSVN to MBARI SVN Repository|CLT:Setting up a SVN Graphical User Interface (GUI)]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository]

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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[Phone conversation with support guys.  I have been working with Ahmad 1 (800) 656-3035 (option 1, then extension 7917).

Eric, Ahmad:

.NET: Microsoft has done their own visual modeling, IBM will not compete.  Software architect does not support .NET, 3rd party can reverse .NET.  Pretty loose coupling. Software architect, fairly close to Together (code visualization), harvesting (reverse), (forward) transformation: java, c++.  ORM - Lightweight: visualization of databases - EJBs are supported (EE 5 will be supported).  Serious data modeling (database architect, separate product). Difference with Together (very similar).  Big difference is what tools it integrates with (testing, requirements). Rational Rose Technical Developer is the place to go for embedded systems.  Moving into RSA (probably 2 years).

Dan Thompson: (Boulder, CO) is my regional sales rep.]]></property>
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<property name="body"><![CDATA[----
h2. Adding your code to MBARI's SVN repository

Here's the standard method of adding a new directory to the subversion repository.

1) On your local machine create the following directory structure
{noformat}
tempdir
`~~ myproject       <-- Replace 'myproject' with the name of your project
   `~~ tags
   `~~ branches
   `~~ trunk
      `~~ agent
      `~~ ctd2007
{noformat}
2) cd to _tempdir_ and run the following command
{{svn import myproject svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject}}

3) To check out _myproject's_ main trunk on another machine you run the command
{{svn co svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject/trunk myproject}} {note:title=Be Careful}


Notice that we've added '/trunk' to the SVN URL above to check out only the trunk (main development line). If you omit '/trunk' you will check out all tags and branches as well as the trunk. {note}

A free on-line guide to SVN is available at [http://svnbook.red-bean.com/]. The most useful svn commands are \\
{noformat}
svn status                            <-- shows you the status of files in your project
svn add some/new/file                 <-- add a new file to version control
svn del some/old/file                 <-- remove a file from version control
svn update                            <-- Get changes from the repository
svn commit -m "some commit message"   <-- commit changes to the repository
svn help
{noformat}
If you find that you can't connect to the svn repository contact Karen Salamy. She may need to give you access permissions.]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | |After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | |Still have not gotten license issues cleared up so have not been able to test|$5500/$9625 float|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[SmartDraw|http://www.smartdraw.com/exp/srd]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]|(/)|(/)|(x)|2.1|Yes, with MDG|(/)|C++, Java, C#, VB.Net, Visual Basic, Delphi, PHP, Python and ActionScript|Visual Studio and Eclipse|Yes, but I don't think automatically|(?)| |There are two pieces, Enterprise Architect(EA) and MDG Technology for SysML.  EA covers UML and MDG adds in SysML support. This one along with Borland one the Jolt award for 2006 for productivity. The EA tools did not really handle code well. Associations with multiplicity did not generate code correctly.|EA=$239,MDG=$100|
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue! Yep, I confirmed it.  You can tell the code generator what kind of collection you wish to use in the UML tool, but in SDE you cannot specify, it always uses object arrays (ouch!). So much for VP.|$1750 (no maint.)|
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | |After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | |Still have not gotten license issues cleared up so have not been able to test|$5500/$9625 float|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[SmartDraw|http://www.smartdraw.com/exp/srd]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]|(/)|(/)|(x)|2.1|Yes, with MDG|(/)|C++, Java, C#, VB.Net, Visual Basic, Delphi, PHP, Python and ActionScript|Visual Studio and Eclipse|Yes, but I don't think automatically|Y|(?)|There are two pieces, Enterprise Architect(EA) and MDG Technology for SysML.  EA covers UML and MDG adds in SysML support. This one along with Borland one the Jolt award for 2006 for productivity. The EA tools did not really handle code well. Associations with multiplicity did not generate code correctly.|EA=$239,MDG=$100|
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue! Yep, I confirmed it.  You can tell the code generator what kind of collection you wish to use in the UML tool, but in SDE you cannot specify, it always uses object arrays (ouch!). So much for VP.|$1750 (no maint.)|
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | |After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | |Still have not gotten license issues cleared up so have not been able to test|$5500/$9625 float|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[SmartDraw|http://www.smartdraw.com/exp/srd]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | |There are two pieces, Enterprise Architect(EA) and MDG Technology for SysML.  EA covers UML and MDG adds in SysML support. This one along with Borland one the Jolt award for 2006 for productivity.| |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue! Yep, I confirmed it.  You can tell the code generator what kind of collection you wish to use in the UML tool, but in SDE you cannot specify, it always uses object arrays (ouch!). So much for VP.|$1750 (no maint.)|
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | |After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | |Still have not gotten license issues cleared up so have not been able to test|$5500/$9625 float|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[SmartDraw|http://www.smartdraw.com/exp/srd]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | |There are two pieces, Enterprise Architect(EA) and MDG Technology for SysML.  EA covers UML and MDG adds in SysML support. This one along with Borland one the Jolt award for 2006 for productivity. The EA tools did not really handle code well. Associations with multiplicity did not generate code correctly.|EA=$239,MDG=$100|
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue! Yep, I confirmed it.  You can tell the code generator what kind of collection you wish to use in the UML tool, but in SDE you cannot specify, it always uses object arrays (ouch!). So much for VP.|$1750 (no maint.)|
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | |After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | |Still have not gotten license issues cleared up so have not been able to test|$5500/$9625 float|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue! Yep, I confirmed it.  You can tell the code generator what kind of collection you wish to use in the UML tool, but in SDE you cannot specify, it always uses object arrays (ouch!). So much for VP.|$1750 (no maint.)|
]]></property>
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<property name="body"><![CDATA[h2.


----
\\
&nbsp;

[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

[*CVS Graphical User Interface (GUI) Client Software Downloads*|CLT:CVS Client Software Downloads] \- {color:#3300cc}Windows, Mac, Linux Systems{color}

[*Setting up&nbsp;the WinCVS GUI*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

[*Command Line Access to CVS Repository&nbsp;(i.e., no GUI)*|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)] *\-* {color:#3300cc}For Linux System Users{color}
\\
\\

\\
&nbsp;
\\
\\
\\
\\
\\
\\

\\
&nbsp;

----]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | |After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | |Still have not gotten license issues cleared up so have not been able to test|$5500/$9625 float|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[SmartDraw|http://www.smartdraw.com/exp/srd]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue! Yep, I confirmed it.  You can tell the code generator what kind of collection you wish to use in the UML tool, but in SDE you cannot specify, it always uses object arrays (ouch!). So much for VP.|$1750 (no maint.)|
]]></property>
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<property name="body"><![CDATA[----
h3. *{+}Welcome to CVS\!+*

CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp;&nbsp;Someone has&nbsp;requested that you be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

h3. \\


h3. +Permissions+

Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. _moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot access _moonjelly_ for any reason, please let me know.

\\
&nbsp;

h3. +Password Access+

Access to the repository requires another (_separate_) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network (_usually with the command prompt, Cygwin Window, or a Linux Terminal_), telnet and login to _moonjelly_ with your standard MBARI password and type the following at the prompt: &nbsp;{color:red}{*}encryptCVSpw{*}{color}
This runs a script that outputs an encrypted version of your password.&nbsp; You may put any password in that you wish - even the same one as your standard MBARI network password.&nbsp; That is up to you.

Next, *{+}Please e-mail me the encrypted text (exactly as shown)+* so that I may add you to the repository password list.&nbsp; I will send you an e-mail when you are able to access the repository.

\\
&nbsp;

h3. *{+}CVS GUIs{+}*

GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the link [Setting up WinCVS_1.2|^Setting_up_WinCVS_1.2_new.doc]. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. Please&nbsp;remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

Regards, - Karen A. Salamy (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | |After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | | |$4000|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue!|$2000 (we get a 10% discount)|
]]></property>
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<property name="body"><![CDATA[----
h3. *{+}Welcome to CVS\!+*

CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp;&nbsp;Someone has&nbsp;requested that you be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

h3. \\


h3. +Permissions+

Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. _moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot access _moonjelly_ for any reason, please let me know.

\\
&nbsp;

h3. +Password Access+

Access to the repository requires another (_separate_) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network (_usually with the command prompt, Cygwin Window, or a Linux Terminal_), {color:#3300ff}{*}telnet{*}{color} and login to _moonjelly_ with your standard MBARI password and type the following at the prompt: &nbsp;{color:red}{*}encryptCVSpw{*}{color}
This runs a script that outputs an encrypted version of your password.&nbsp; You may put any password in that you wish - even the same one as your standard MBARI network password.&nbsp; That is up to you.

Next, *{+}Please e-mail me the encrypted text (exactly as shown)+* so that I may add you to the repository password list.&nbsp; I will send you an e-mail when you are able to access the repository.

\\
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h3. *{+}CVS GUIs{+}*

GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the link [Setting up WinCVS_1.2|^Setting_up_WinCVS_1.2_new.doc]. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. Please&nbsp;remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

Regards, - Karen A. Salamy (_MBARI CVS administrator)_ \- salamy@mbari.org
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]| | | | | | | | | | | |After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | |Still have not gotten license issues cleared up so have not been able to test|$5500/$9625 float|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]| | | | | | | | | | | | | |
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue!|$2000 (we get a 10% discount)|
]]></property>
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<property name="body"><![CDATA[h2.


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h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).&nbsp; {color:#ff0033}{*}NOTE:*{color} {color:#ff0033}In the rare event the administrator is on vacation or unavailable, please&nbsp;submit your CVS request to the IS Remedy page at:&nbsp;{color} [https://ishelp.shore.mbari.org/helpdesk/WebObjects/Helpdesk] {color:#ff0033}and it will be assigned by IS appropriately based on urgency level.{color}

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;CVS command Line Reference. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/.&nbsp];

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

\\
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[Welcome to CVS\!|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

[CVS Graphical User Interface (GUI) Client Software Downloads|CLT:CVS Client Software Downloads] \- {color:#3300cc}Windows, Mac, Linux Systems{color}

[Setting up&nbsp;the WinCVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]

[Adding code to CVS Repository with WinCVS GUI|CLT:Adding code to CVS Repository with WinCVS GUI]

[Command Line Access to CVS Repository&nbsp;(i.e., no GUI)|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)] *\-* {color:#3300cc}For Linux System Users{color}

[View the CVS Repository|http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/ ]\\
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[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

[*CVS Graphical User Interface (GUI) Client Software Downloads*|CLT:CVS Client Software Downloads] \- {color:#3300cc}Windows, Mac, Linux Systems{color}

[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

[*Command Line Access to CVS Repository&nbsp;(i.e., no GUI)*|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)] *\-* {color:#3300cc}For Linux System Users{color}
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<property name="body"><![CDATA[h2.


----
h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).&nbsp;

{color:#ff0033}{*}NOTE:*{color} {color:#ff0033}In the rare event the administrator is on vacation or unavailable, please&nbsp;submit your CVS request to the IS Remedy page at:&nbsp;{color} [https://ishelp.shore.mbari.org/helpdesk/WebObjects/Helpdesk] {color:#ff0033}and it will be assigned by IS appropriately based on urgency level.{color}

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;CVS command Line Reference. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/.&nbsp];

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

\\
&nbsp;

[Welcome to CVS\!|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

[CVS Graphical User Interface (GUI) Client Software Downloads|CLT:CVS Client Software Downloads] \- {color:#3300cc}Windows, Mac, Linux Systems{color}

[Setting up&nbsp;the WinCVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]

[Adding code to CVS Repository with WinCVS GUI|CLT:Adding code to CVS Repository with WinCVS GUI]

[Command Line Access to CVS Repository&nbsp;(i.e., no GUI)|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)] *\-* {color:#3300cc}For Linux System Users{color}

[View the CVS Repository|http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/ ]\\
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[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

[*CVS Graphical User Interface (GUI) Client Software Downloads*|CLT:CVS Client Software Downloads]

[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

[*Command Line Access to CVS Repository&nbsp;(i.e., no GUI)*|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)] *\-* For Linux System Users
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----
h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;CVS command Line Reference. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/.&nbsp];

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

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[Welcome to CVS\!|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

[CVS Graphical User Interface (GUI) Client Software Downloads|CLT:CVS Client Software Downloads] \- {color:#3300cc}Windows, Mac, Linux Systems{color}

[Setting up&nbsp;the WinCVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]

[Adding code to CVS Repository with WinCVS GUI|CLT:Adding code to CVS Repository with WinCVS GUI]

[Command Line Access to CVS Repository&nbsp;(i.e., no GUI)|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)] *\-* {color:#3300cc}For Linux System Users{color}

[View the CVS Repository|http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/ ]\\
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[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

[*CVS Graphical User Interface (GUI) Client Software Downloads*|CLT:CVS Client Software Downloads]

[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

[*Command Line Access to CVS Repository&nbsp;(i.e., no GUI)*|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)] *\-* {color:#ff0000}For Linux System Users{color}
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----
h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

*NOTE:* In the rare event the administrator is on vacation or unavailable, please&nbsp;submit your CVS request to the IS Remedy page at:&nbsp; https://ishelp.shore.mbari.org/helpdesk/WebObjects/Helpdesk and it will be assigned by IS appropriately based on urgency level.

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;CVS command Line Reference. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/.&nbsp];

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

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[Welcome to CVS\!|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

[CVS Graphical User Interface (GUI) Client Software Downloads|CLT:CVS Client Software Downloads] \- {color:#3300cc}Windows, Mac, Linux Systems{color}

[Setting up&nbsp;the WinCVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]

[Adding code to CVS Repository with WinCVS GUI|CLT:Adding code to CVS Repository with WinCVS GUI]

[Command Line Access to CVS Repository&nbsp;(i.e., no GUI)|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)] *\-* {color:#3300cc}For Linux System Users{color}

[View the CVS Repository|http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/ ]\\
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[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

[*CVS Graphical User Interface (GUI) Client Software Downloads*\|CLT:CVS Client Software Downloads]

[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]\*

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

[*Command Line Access to CVS Repository&nbsp;(i.e., no GUI)*|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)]\* *\-* For Linux System Users
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[*CVS Graphical User Interface (GUI) Client Software Downloads*|CLT:CVS Client Software Downloads]

[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]\*

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

[*Command Line Access to CVS Repository&nbsp;(i.e., no GUI)*|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)]\* *\-* For Linux System Users
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]|(/)|(/)|(/)|2.0|(x)|(/)|Java,C++| | | | |After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | |Still have not gotten license issues cleared up so have not been able to test|$5500/$9625 float|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[SmartDraw|http://www.smartdraw.com/exp/srd]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]|(/)|(/)|(x)|2.1|Yes, with MDG|(/)|C++, Java, C#, VB.Net, Visual Basic, Delphi, PHP, Python and ActionScript|Visual Studio and Eclipse|Yes, but I don't think automatically|Y|(?)|There are two pieces, Enterprise Architect(EA) and MDG Technology for SysML.  EA covers UML and MDG adds in SysML support. This one along with Borland one the Jolt award for 2006 for productivity. The EA tools did not really handle code well. Associations with multiplicity did not generate code correctly.|EA=$239,MDG=$100|
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue! Yep, I confirmed it.  You can tell the code generator what kind of collection you wish to use in the UML tool, but in SDE you cannot specify, it always uses object arrays (ouch!). So much for VP.|$1750 (no maint.)|
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[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

{color:#000000}*[{color:#000000}{*}CVS Graphical User Interface (GUI) Client Software Downloads{*}{color}|CLT:CVS Client Software Downloads]*{color}

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

*[*Command Line Access to CVS Repository&nbsp;(i.e., no GUI)*|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)]* *\-* {color:#ff0000}For Linux System Users{color}
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test.|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]|(/)|(/)|(/)|2.0|(x)|(/)|Java,C++|Eclipse|(/) The best by far|(/) Java,C++|(?)|After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | |Still have not gotten license issues cleared up so have not been able to test|$5500/$9625 float|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[SmartDraw|http://www.smartdraw.com/exp/srd]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]|(/)|(/)|(x)|2.1|Yes, with MDG|(/)|C++, Java, C#, VB.Net, Visual Basic, Delphi, PHP, Python and ActionScript|Visual Studio and Eclipse|Yes, but I don't think automatically|Y|(?)|There are two pieces, Enterprise Architect(EA) and MDG Technology for SysML.  EA covers UML and MDG adds in SysML support. This one along with Borland one the Jolt award for 2006 for productivity. The EA tools did not really handle code well. Associations with multiplicity did not generate code correctly.|EA=$239,MDG=$100|
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue! Yep, I confirmed it.  You can tell the code generator what kind of collection you wish to use in the UML tool, but in SDE you cannot specify, it always uses object arrays (ouch!). So much for VP.|$1750 (no maint.)|
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[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

{color:#000000}[{color:#000000}{*}CVS Graphical User Interface (GUI) Client Software Downloads{*}{color}|CLT:CVS Client Software Downloads]{color}{color:#000000}&nbsp;\- Windows, Macs, Linux Systems{color}

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

*[*Command Line Access to CVS Repository&nbsp;(i.e., no GUI)*|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)]* *\-* {color:#ff0000}For Linux System Users{color}
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{color:#000000}*[{color:#000000}{*}CVS Graphical User Interface (GUI) Client Software Downloads{*}{color}|CLT:CVS Client Software Downloads]*{color} {color:#000000}*\- Windows, Macs, Linux Systems{*}{color}

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

*[*Command Line Access to CVS Repository&nbsp;(i.e., no GUI)*|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)]* *\-* {color:#ff0000}For Linux System Users{color}
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit their respective websites.

Contact Kevin Gomes [mailto:kgomes@mbari.org], Brian Schlining [mailto:brian@mbari.org] or Kent Headley [mailto:headley@mbari.org] with questions or permission requests for certain tools.

{tip:title=External Availability}
Please note that Confluence, JIRA, and Alfresco are all available outside the MBARI firewall and can have external collaborator accounts that are not MBARI accounts.  This was a desirable feature of these tools and allows us to externally collaborate without risking security breaches at MBARI.
{tip}

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.
----
h3. Authentication and Single Sign On With Crowd

[Crowd|http://www.atlassian.com/crowd] is an authentication tool that is developed by [Atlassian|http://www.atlassian.com] and is provided to MBARI under a community/non-profit license.  It provides an internal user database so we can create external user accounts that can then be linked to other applications such as JIRA and Confluence.  It also connects to our internal MBARI user database using LDAP so that MBARI users can have Single Sign on capability across multiple applications.

Links for Crowd at MBARI:
* [Crowd Web Application|http://oceana.mbari.org:8095/crowd]
* [Documentation of MBARI Crowd Installation|MBARI Crowd Installation]

----
h3. Content Management with [Alfresco|https://alfresco.mbari.org/alfresco]

Alfresco is a Content Management System (CMS) intended to replace the Project Library on Tornado as the repository for MBARI project documentation. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

{info:title=Accounting Creates Projects in Alfresco}
One of the main benefits of Alfresco is that it can interact with our accounting system in an automated fashion. Because of this, we have the accounting system currently creating project spaces and directory structures in Alfresco automatically.  This allows the accounting software to then export all accounting activity (PDFs of AMEX, PO's, etc.) to the Alfresco spaces automatically.
{info}

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password without using "shore\" in front) to see the project library materials. The *Projects* folder is the space that contains the content for projects at MBARI.

To create a short cut to the Projects folder (or any folder), enter that folder, then select "More Actions/View Details", then "Create Shortcut" (on the right side of the page).  This will create a shortcut that will be available in the "Shelf".  To view the shortcuts in your "Shelf", click on the down arrow next to "Navigtor" on the left hand sidebar menu, then select "Shelf" and you will see your created shortcuts.

Here are some useful links related to MBARI's installation of Alfresco:
* [Alfresco's Homepage|http://www.alfresco.com/]
* [Alfresco's Developer Home Page|http://wiki.alfresco.com/wiki/Main_Page]
* [Alfresco's Enterprise Customer Portal|https://network.alfresco.com/extranet/]
* [Deployment Information for MBARI's Alfresco Installation|Deployment Information]
* [Installation Notes]
* [alfresco.mbari.org Installation Notes]
* [alfresco-test.shore.mbari.org Installation Notes]

----
h3. WIKI Collaboration Pages ([Confluence|https://oceana.mbari.org/confluence])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

# [Installation Notes]

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts an externally accessable Maven repository at [https://oceana.mbari.org/maven2], an internal repository at [http://seaspray.shore.mbari.org:8082/archiva/repository/internal/] and a repository manager at [http://seaspray.shore.mbari.org:8082/archiva]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modeling with UML (JBuilder 2008 Enterprise)

You can download JBuilder 2008 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded and installed, you need to copy the following [.slip|https://alfresco.mbari.org/alfresco/webdav/Engineering/Tools/Collaboration%20Tools/CodeGear%20JBuilder/concurrent_31474.slip] file to the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit their respective websites.

Contact Kevin Gomes [mailto:kgomes@mbari.org], Brian Schlining [mailto:brian@mbari.org] or Kent Headley [mailto:headley@mbari.org] with questions or permission requests for certain tools.

{tip:title=External Availability}
Please note that Confluence, JIRA, and Alfresco are all available outside the MBARI firewall and can have external collaborator accounts that are not MBARI accounts.  This was a desirable feature of these tools and allows us to externally collaborate without risking security breaches at MBARI.
{tip}

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.
----
h3. Authentication and Single Sign On With Crowd

[Crowd|http://www.atlassian.com/crowd] is an authentication tool that is developed by [Atlassian|http://www.atlassian.com] and is provided to MBARI under a community/non-profit license.  It provides an internal user database so we can create external user accounts that can then be linked to other applications such as JIRA and Confluence.  It also connects to our internal MBARI user database using LDAP so that MBARI users can have Single Sign on capability across multiple applications.

Links for Crowd at MBARI:
* [Crowd Web Application|http://oceana.mbari.org:8095/crowd]
* [Documentation of MBARI Crowd Installation|MBARI Crowd Installation]

----
h3. Content Management with [Alfresco|https://alfresco.mbari.org/alfresco]

Alfresco is a Content Management System (CMS) intended to replace the Project Library on Tornado as the repository for MBARI project documentation. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

{info:title=Accounting Creates Projects in Alfresco}
One of the main benefits of Alfresco is that it can interact with our accounting system in an automated fashion. Because of this, we have the accounting system currently creating project spaces and directory structures in Alfresco automatically.  This allows the accounting software to then export all accounting activity (PDFs of AMEX, PO's, etc.) to the Alfresco spaces automatically.
{info}

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password without using "shore\" in front) to see the project library materials. The *Projects* folder is the space that contains the content for projects at MBARI.

To create a short cut to the Projects folder (or any folder), enter that folder, then select "More Actions/View Details", then "Create Shortcut" (on the right side of the page).  This will create a shortcut that will be available in the "Shelf".  To view the shortcuts in your "Shelf", click on the down arrow next to "Navigtor" on the left hand sidebar menu, then select "Shelf" and you will see your created shortcuts.

Here are some useful links related to MBARI's installation of Alfresco:
* [Alfresco's Homepage|http://www.alfresco.com/]
* [Alfresco's Developer Home Page|http://wiki.alfresco.com/wiki/Main_Page]
* [Alfresco's Enterprise Customer Portal|https://network.alfresco.com/extranet/]
* [Deployment Information for MBARI's Alfresco Installation|Deployment Information]
* [Installation Notes]
* [alfresco.mbari.org Installation Notes]
* [alfresco-test.shore.mbari.org Installation Notes]

----
h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts an externally accessable Maven repository at [https://oceana.mbari.org/maven2], an internal repository at [http://seaspray.shore.mbari.org:8082/archiva/repository/internal/] and a repository manager at [http://seaspray.shore.mbari.org:8082/archiva]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modeling with UML (JBuilder 2008 Enterprise)

You can download JBuilder 2008 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded and installed, you need to copy the following [.slip|https://alfresco.mbari.org/alfresco/webdav/Engineering/Tools/Collaboration%20Tools/CodeGear%20JBuilder/concurrent_31474.slip] file to the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[h2.


----
\\
&nbsp;

[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

*[*Command Line Access to CVS Repository&nbsp;(i.e., no GUI)*|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)]* *\-* {color:#ff0000}For Linux System Users{color}
\\
\\

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----]]></property>
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<property name="body"><![CDATA[h2.


----
\\
&nbsp;

[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

*[*Command Line Access to CVS Repository&nbsp;(i.e., no GUI)*|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)]* *\-* {color:#ff0000}{*}For Linux Users{*}{color}
\\
\\

\\
&nbsp;
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----]]></property>
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<property name="body"><![CDATA[h2.


----
\\
&nbsp;

[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

[*Setup to access CVS Repository with Command line instead of GUI (Linux users)*|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)]\\
\\

\\
&nbsp;\\ \\ \\ \\ \\ \\

\\
&nbsp;

----]]></property>
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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on *{+}Linux systems{+}* with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your account, you will need to log in to the CVS Repository.&nbsp; You should only have to do this once in the window you are using during&nbsp;each session.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}cvs login{*}{color}\\
\\
\\

You should get the following response from the computer:

*Logging in to :pserver:*{*}{_}your_userName{_}{*}*@moonjelly.shore.mbari.org:2401/home/cvs*
*CVS password:*
\\

Enter your CVS password at the prompt.&nbsp; If you have entered the correct password you will be returned to a &nbsp;*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$*&nbsp;&nbsp;prompt.&nbsp; You are now logged in and can access project modules on the system.&nbsp; If you receive a login error from the system, re-check your password as forgotten passwords&nbsp;is the number one problem experienced by CVS users.&nbsp; If the problem persists, please contact Karen Salamy (the CVS Repository Administrator):&nbsp; {color:#3300cc}salamy@mbari.org&nbsp;&nbsp;{color} {color:#000000}.{color}
\\
\\
\\

----
h3. CVS Command Line Usage

\\

\\
CVS has an *enormous* number of commands and options available. Usage of Command Lines for CVS requires familiarization with the command calls.&nbsp;&nbsp;A common link is&nbsp;provided below to help get started:

*[*CVS Command Line Reference Guide*|https://oceana.mbari.org/confluence/download/attachments/54/CVS-commandline-reference.pdf?version=1]*

\\
\\

----
h3. &nbsp;Additional Usage Guidance

\\
The general format of CVS commands is:

% cvsgeneral-optionscommand-namecommand-specific-optionsfilename

Here's how to get help:
| cvs \--help-commands | Show all of the commands |
| cvs \--help-options | Shows the "global" options, which apply to all commands. The most useful of these is \-n, which doesn't execute anything that will change files stored on the disk, but shows what work it would have done. |
| cvs \-H command | Show the command-specific options. |

h3. Task Reference

|| Action || How to do it. ||
| Sync your tree with the repository. \\
See what files are modified or haven't been checked in | cvs update(sample) |
| See complete revision history for a file | cvs log filename(sample) |
| See revision comment for one revision | cvs log \-r1.5 filename |
| See the differences between a file and its last checked in version | cvs diff filename |
| See the differneces between two checked-in revisions of a file | cvs diff \-r1.4 \-r1.7 filename(sample) |
| See who modified each line of a file, with what revision | cvs annotate filename(sample) This is handy when you see a line of really bogus code and you want to know who was reponsible. |
| Add a new file to the repository | Create the file \\
cvs add filename \\
cvs commit \-m "Initial Revision" filename |
| Add a new binary file to the repository | Create the file \\
cvs add \-kb filename \\
cvs commit \-m "Initial Revision" filename A "binary file" won't have CVS keyword expansion performed on it. \\ |
| Add a new directory to the project | cd to the directory's parent cvs add directoryname |
| Checking a file's changes into the repository. | cvs commit \-m "check-in comment" filenameIf your check-in comment is more than one line, leave off the the \-m option and use the editor that is brought up. |
| Revert a file to its last checked-in revision | Remove the file \\
cvs update filename |
| Add a whole directory tree as a new project | cdto the project directory \\
cvs import \-m "project name" directory "ArsDigita" "initial-development" Note that this does not change directory into a CVS-controlled tree. You'll need to remove the tree and check it out. |
| Check out a whole project | cvs checkout project-name |
| Label a tree for concurrent development | cd to the parent directory of your tree \\
cvs tag \-R \-b labelname This will use the currently-checked-out versions of the files as they exist in your directory tree. \\
The \-b argument means that this tag is a "branch" tag, meaning that someone can check out a new tree based on this tag and do development. \\
If you omit the \-b, the label will be a "sticky" tag, meaning that someone won't be able to check in new changes under that label. See the notes on Labeling and Branching |
| Check out a tree based on a label | cvs checkout \-r labelname projectnameIf labelname was created as a "branch" tag, then you can check in changes without affecting anyone using the development tip. Otherwise files are considered "sticky" and changes cannot be checked in. |
| Change a file to be treated as a binary file after it's been added | cvs admin \-kb filename A "binary file" won't have CVS keyword expansion performed on it. |

h3. \\

\\]]></property>
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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on *{+}Linux systems{+}* with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your account, you will need to log in to the CVS Repository.&nbsp; You should only have to do this once in the window you are using during&nbsp;each session.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}cvs login{*}{color}\\
\\
\\

You should get the following response from the computer:

*Logging in to :pserver:*{*}{_}your_userName{_}{*}*@moonjelly.shore.mbari.org:2401/home/cvs*
*CVS password:*
\\

Enter your CVS password at the prompt.&nbsp; If you have entered the correct password you will be returned to a &nbsp;*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$*&nbsp;&nbsp;prompt.&nbsp; You are now logged in and can access project modules on the system.&nbsp; If you receive a login error from the system, re-check your password as forgotten passwords&nbsp;is the number one problem experienced by CVS users.&nbsp; If the problem persists, please contact Karen Salamy (the CVS Repository Administrator):&nbsp; {color:#3300cc}salamy@mbari.org&nbsp;&nbsp;{color} {color:#000000}.{color}
\\
\\
\\

----
h3. CVS Command Line Usage

\\

\\
CVS has an *enormous* number of commands and options available. Usage of Command Lines for CVS requires familiarization with the command calls.&nbsp;&nbsp;A common link is&nbsp;provided below to help get started:

*[*CVS Command Line Reference Guide*|https://oceana.mbari.org/confluence/download/attachments/54/CVS-commandline-reference.pdf?version=1]*

\\ \\

----
h3. &nbsp;&nbsp;


h3. Additional Usage Guidance

\\
The general format of CVS commands is:

% cvsgeneral-optionscommand-namecommand-specific-optionsfilename

Here's how to get help:
| cvs \--help-commands | Show all of the commands |
| cvs \--help-options | Shows the "global" options, which apply to all commands. The most useful of these is \-n, which doesn't execute anything that will change files stored on the disk, but shows what work it would have done. |
| cvs \-H command | Show the command-specific options. |

h3. Task Reference

|| Action || How to do it. ||
| Sync your tree with the repository. \\
See what files are modified or haven't been checked in | cvs update(sample) |
| See complete revision history for a file | cvs log filename(sample) |
| See revision comment for one revision | cvs log \-r1.5 filename |
| See the differences between a file and its last checked in version | cvs diff filename |
| See the differneces between two checked-in revisions of a file | cvs diff \-r1.4 \-r1.7 filename(sample) |
| See who modified each line of a file, with what revision | cvs annotate filename(sample) This is handy when you see a line of really bogus code and you want to know who was reponsible. |
| Add a new file to the repository | Create the file \\
cvs add filename \\
cvs commit \-m "Initial Revision" filename |
| Add a new binary file to the repository | Create the file \\
cvs add \-kb filename \\
cvs commit \-m "Initial Revision" filename A "binary file" won't have CVS keyword expansion performed on it. \\ |
| Add a new directory to the project | cd to the directory's parent cvs add directoryname |
| Checking a file's changes into the repository. | cvs commit \-m "check-in comment" filenameIf your check-in comment is more than one line, leave off the the \-m option and use the editor that is brought up. |
| Revert a file to its last checked-in revision | Remove the file \\
cvs update filename |
| Add a whole directory tree as a new project | cdto the project directory \\
cvs import \-m "project name" directory "ArsDigita" "initial-development" Note that this does not change directory into a CVS-controlled tree. You'll need to remove the tree and check it out. |
| Check out a whole project | cvs checkout project-name |
| Label a tree for concurrent development | cd to the parent directory of your tree \\
cvs tag \-R \-b labelname This will use the currently-checked-out versions of the files as they exist in your directory tree. \\
The \-b argument means that this tag is a "branch" tag, meaning that someone can check out a new tree based on this tag and do development. \\
If you omit the \-b, the label will be a "sticky" tag, meaning that someone won't be able to check in new changes under that label. See the notes on Labeling and Branching |
| Check out a tree based on a label | cvs checkout \-r labelname projectnameIf labelname was created as a "branch" tag, then you can check in changes without affecting anyone using the development tip. Otherwise files are considered "sticky" and changes cannot be checked in. |
| Change a file to be treated as a binary file after it's been added | cvs admin \-kb filename A "binary file" won't have CVS keyword expansion performed on it. |

h3. \\

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h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on *{+}Linux systems{+}* with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your account, you will need to log in to the CVS Repository.&nbsp; You should only have to do this once in the window you are using during&nbsp;each session.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}cvs login{*}{color}\\
\\
\\

You should get the following response from the computer:

*Logging in to :pserver:*{*}{_}your_userName{_}{*}*@moonjelly.shore.mbari.org:2401/home/cvs*
*CVS password:*
\\

Enter your CVS password at the prompt.&nbsp; If you have entered the correct password you will be returned to a &nbsp;*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$*&nbsp;&nbsp;prompt.&nbsp; You are now logged in and can access project modules on the system.&nbsp; If you receive a login error from the system, re-check your password as forgotten passwords&nbsp;is the number one problem experienced by CVS users.&nbsp; If the problem persists, please contact Karen Salamy (the CVS Repository Administrator):&nbsp; {color:#3300cc}salamy@mbari.org&nbsp;&nbsp;{color} {color:#000000}.{color}
\\
\\
\\

----
h3. CVS Command Line Usage

\\

\\
CVS has an *enormous* number of commands and options available. Usage of Command Lines for CVS requires familiarization with the command calls.&nbsp;&nbsp;A common link is&nbsp;provided below to help get started:

*[*CVS Command Line Reference Guide*|https://oceana.mbari.org/confluence/download/attachments/54/CVS-commandline-reference.pdf?version=1]* \\

----\\ \\

\\
*&nbsp;*\\ \\

\\
&nbsp;

\\

h3. Additional Usage Guidance

The general format of CVS commands is:

% cvsgeneral-optionscommand-namecommand-specific-optionsfilename

Here's how to get help:
| cvs \--help-commands | Show all of the commands |
| cvs \--help-options | Shows the "global" options, which apply to all commands. The most useful of these is \-n, which doesn't execute anything that will change files stored on the disk, but shows what work it would have done. |
| cvs \-H command | Show the command-specific options. |

h3. Task Reference

|| Action || How to do it. ||
| Sync your tree with the repository. \\
See what files are modified or haven't been checked in | cvs update(sample) |
| See complete revision history for a file | cvs log filename(sample) |
| See revision comment for one revision | cvs log \-r1.5 filename |
| See the differences between a file and its last checked in version | cvs diff filename |
| See the differneces between two checked-in revisions of a file | cvs diff \-r1.4 \-r1.7 filename(sample) |
| See who modified each line of a file, with what revision | cvs annotate filename(sample) This is handy when you see a line of really bogus code and you want to know who was reponsible. |
| Add a new file to the repository | Create the file \\
cvs add filename \\
cvs commit \-m "Initial Revision" filename |
| Add a new binary file to the repository | Create the file \\
cvs add \-kb filename \\
cvs commit \-m "Initial Revision" filename A "binary file" won't have CVS keyword expansion performed on it. \\ |
| Add a new directory to the project | cd to the directory's parent cvs add directoryname |
| Checking a file's changes into the repository. | cvs commit \-m "check-in comment" filenameIf your check-in comment is more than one line, leave off the the \-m option and use the editor that is brought up. |
| Revert a file to its last checked-in revision | Remove the file \\
cvs update filename |
| Add a whole directory tree as a new project | cdto the project directory \\
cvs import \-m "project name" directory "ArsDigita" "initial-development" Note that this does not change directory into a CVS-controlled tree. You'll need to remove the tree and check it out. |
| Check out a whole project | cvs checkout project-name |
| Label a tree for concurrent development | cd to the parent directory of your tree \\
cvs tag \-R \-b labelname This will use the currently-checked-out versions of the files as they exist in your directory tree. \\
The \-b argument means that this tag is a "branch" tag, meaning that someone can check out a new tree based on this tag and do development. \\
If you omit the \-b, the label will be a "sticky" tag, meaning that someone won't be able to check in new changes under that label. See the notes on Labeling and Branching |
| Check out a tree based on a label | cvs checkout \-r labelname projectnameIf labelname was created as a "branch" tag, then you can check in changes without affecting anyone using the development tip. Otherwise files are considered "sticky" and changes cannot be checked in. |
| Change a file to be treated as a binary file after it's been added | cvs admin \-kb filename A "binary file" won't have CVS keyword expansion performed on it. |

h3. \\

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h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on *{+}Linux systems{+}* with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your account, you will need to log in to the CVS Repository.&nbsp; You should only have to do this once in the window you are using during&nbsp;each session.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}cvs login{*}{color}\\
\\
\\

You should get the following response from the computer:

*Logging in to :pserver:*{*}{_}your_userName{_}{*}*@moonjelly.shore.mbari.org:2401/home/cvs*
*CVS password:*
\\

Enter your CVS password at the prompt.&nbsp; If you have entered the correct password you will be returned to a &nbsp;*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$*&nbsp;&nbsp;prompt.&nbsp; You are now logged in and can access project modules on the system.&nbsp; If you receive a login error from the system, re-check your password as forgotten passwords&nbsp;is the number one problem experienced by CVS users.&nbsp; If the problem persists, please contact Karen Salamy (the CVS Repository Administrator):&nbsp; {color:#3300cc}salamy@mbari.org&nbsp;&nbsp;{color} {color:#000000}.{color}
\\
\\
\\

----
h3. CVS Command Line Usage

\\

\\
CVS has an *enormous* number of commands and options available. Usage of Command Lines for CVS requires familiarization with the command calls.&nbsp;&nbsp;A common link is&nbsp;provided below to help get started:

*[*CVS Command Line Reference Guide*|https://oceana.mbari.org/confluence/download/attachments/54/CVS-commandline-reference.pdf?version=1]*
\\
*&nbsp;*

\---\-

----\\

\\

h3. Additional Usage Guidance

The general format of CVS commands is:

% cvsgeneral-optionscommand-namecommand-specific-optionsfilename

Here's how to get help:
| cvs \--help-commands | Show all of the commands |
| cvs \--help-options | Shows the "global" options, which apply to all commands. The most useful of these is \-n, which doesn't execute anything that will change files stored on the disk, but shows what work it would have done. |
| cvs \-H command | Show the command-specific options. |

h3. Task Reference

|| Action || How to do it. ||
| Sync your tree with the repository. \\
See what files are modified or haven't been checked in | cvs update(sample) |
| See complete revision history for a file | cvs log filename(sample) |
| See revision comment for one revision | cvs log \-r1.5 filename |
| See the differences between a file and its last checked in version | cvs diff filename |
| See the differneces between two checked-in revisions of a file | cvs diff \-r1.4 \-r1.7 filename(sample) |
| See who modified each line of a file, with what revision | cvs annotate filename(sample) This is handy when you see a line of really bogus code and you want to know who was reponsible. |
| Add a new file to the repository | Create the file \\
cvs add filename \\
cvs commit \-m "Initial Revision" filename |
| Add a new binary file to the repository | Create the file \\
cvs add \-kb filename \\
cvs commit \-m "Initial Revision" filename A "binary file" won't have CVS keyword expansion performed on it. \\ |
| Add a new directory to the project | cd to the directory's parent cvs add directoryname |
| Checking a file's changes into the repository. | cvs commit \-m "check-in comment" filenameIf your check-in comment is more than one line, leave off the the \-m option and use the editor that is brought up. |
| Revert a file to its last checked-in revision | Remove the file \\
cvs update filename |
| Add a whole directory tree as a new project | cdto the project directory \\
cvs import \-m "project name" directory "ArsDigita" "initial-development" Note that this does not change directory into a CVS-controlled tree. You'll need to remove the tree and check it out. |
| Check out a whole project | cvs checkout project-name |
| Label a tree for concurrent development | cd to the parent directory of your tree \\
cvs tag \-R \-b labelname This will use the currently-checked-out versions of the files as they exist in your directory tree. \\
The \-b argument means that this tag is a "branch" tag, meaning that someone can check out a new tree based on this tag and do development. \\
If you omit the \-b, the label will be a "sticky" tag, meaning that someone won't be able to check in new changes under that label. See the notes on Labeling and Branching |
| Check out a tree based on a label | cvs checkout \-r labelname projectnameIf labelname was created as a "branch" tag, then you can check in changes without affecting anyone using the development tip. Otherwise files are considered "sticky" and changes cannot be checked in. |
| Change a file to be treated as a binary file after it's been added | cvs admin \-kb filename A "binary file" won't have CVS keyword expansion performed on it. |

h3. \\

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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on *{+}Linux systems{+}* with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your account, you will need to log in to the CVS Repository.&nbsp; You should only have to do this once in the window you are using during&nbsp;each session.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}cvs login{*}{color}\\
\\
\\

You should get the following response from the computer:

*Logging in to :pserver:*{*}{_}your_userName{_}{*}*@moonjelly.shore.mbari.org:2401/home/cvs*
*CVS password:*
\\

Enter your CVS password at the prompt.&nbsp; If you have entered the correct password you will be returned to a &nbsp;*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$*&nbsp;&nbsp;prompt.&nbsp; You are now logged in and can access project modules on the system.&nbsp; If you receive a login error from the system, re-check your password as forgotten passwords&nbsp;is the number one problem experienced by CVS users.&nbsp; If the problem persists, please contact Karen Salamy (the CVS Repository Administrator):&nbsp; {color:#3300cc}salamy@mbari.org&nbsp;&nbsp;{color} {color:#000000}.{color}
\\

----
h3. CVS Command Line Usage


h3. CVS Command Line Usage

\\
\\

h3. \\

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h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on *{+}Linux systems{+}* with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your account, you will need to log in to the CVS Repository.&nbsp; You should only have to do this once in the window you are using during&nbsp;each session.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}cvs login{*}{color}\\
\\
\\

You should get the following response from the computer:

*Logging in to :pserver:*{*}{_}your_userName{_}{*}*@moonjelly.shore.mbari.org:2401/home/cvs*
*CVS password:*
\\

Enter your CVS password at the prompt.&nbsp; If you have entered the correct password you will be returned to a &nbsp;*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$*&nbsp;&nbsp;prompt.&nbsp; You are now logged in and can access project modules on the system.&nbsp; If you receive a login error from the system, re-check your password as forgotten passwords&nbsp;is the number one problem experienced by CVS users.&nbsp; If the problem persists, please contact Karen Salamy (the CVS Repository Administrator):&nbsp; {color:#3300cc}salamy@mbari.org&nbsp;&nbsp;{color} {color:#000000}.{color}
\\ \\

----
h3. CVS Command Line Usage


h3. CVS Command Line Usage

\\
\\

h3. \\

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h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on *{+}Linux systems{+}* with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your account, you will need to log in to the CVS Repository.&nbsp; You should only have to do this once in the window you are using during&nbsp;each session.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}cvs login{*}{color}\\
\\
\\

You should get the following response from the computer:

*Logging in to :pserver:*{*}{_}your_userName{_}{*}*@moonjelly.shore.mbari.org:2401/home/cvs*
*CVS password:*
\\

Enter your CVS password at the prompt.&nbsp; If you have entered the correct password you will be returned to a &nbsp;*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$*&nbsp;&nbsp;prompt.&nbsp; You are now logged in and can access project modules on the system.&nbsp; If you receive a login error from the system, re-check your password as forgotten passwords&nbsp;is the number one problem experienced by CVS users.&nbsp; If the problem persists, please contact Karen Salamy (the CVS Repository Administrator):&nbsp; {color:#3300cc}salamy@mbari.org&nbsp;&nbsp;{color} {color:#000000}.{color}
\\
\\ \\

----
h3. CVS Command Line Usage
\\

\\
CVS has an *enormous* number of commands and options available. Usage of Command Lines for CVS requires familiarization with the command calls.&nbsp;&nbsp;A common link is&nbsp;provided below to help get started:

*[*CVS Command Line Reference Guide*|https://oceana.mbari.org/confluence/download/attachments/54/CVS-commandline-reference.pdf?version=1]*\\ *&nbsp;*

----\\

h3. Additional Usage Guidance

The general format of CVS commands is:

% cvsgeneral-optionscommand-namecommand-specific-optionsfilename

Here's how to get help:
| cvs --help-commands | Show all of the commands |
| cvs --help-options | Shows the "global" options, which apply to all commands. The most useful of these is -n, which doesn't execute anything that will change files stored on the disk, but shows what work it would have done. |
| cvs -H command | Show the command-specific options. |

h3. Task Reference
|| Action || How to do it. ||
| Sync your tree with the repository.\\
 See what files are modified or haven't been checked in | cvs update(sample) |
| See complete revision history for a file | cvs log filename(sample) |
| See revision comment for one revision | cvs log -r1.5 filename |
| See the differences between a file and its last checked in version | cvs diff filename |
| See the differneces between two checked-in revisions of a file | cvs diff -r1.4 -r1.7 filename(sample) |
| See who modified each line of a file, with what revision | cvs annotate filename(sample) This is handy when you see a line of really bogus code and you want to know who was reponsible. |
| Add a new file to the repository | Create the file\\
 cvs add filename\\
 cvs commit -m "Initial Revision" filename |
| Add a new binary file to the repository | Create the file\\
 cvs add -kb filename\\
 cvs commit -m "Initial Revision" filename A "binary file" won't have CVS keyword expansion performed on it.\\ |
| Add a new directory to the project | cd to the directory's parent cvs add directoryname |
| Checking a file's changes into the repository. | cvs commit -m "check-in comment" filenameIf your check-in comment is more than one line, leave off the the -m option and use the editor that is brought up. |
| Revert a file to its last checked-in revision | Remove the file\\
 cvs update filename |
| Add a whole directory tree as a new project | cdto the project directory \\
 cvs import -m "project name" directory "ArsDigita" "initial-development" Note that this does not change directory into a CVS-controlled tree. You'll need to remove the tree and check it out. |
| Check out a whole project | cvs checkout project-name |
| Label a tree for concurrent development | cd to the parent directory of your tree\\
 cvs tag -R -b labelname This will use the currently-checked-out versions of the files as they exist in your directory tree. \\
The -b argument means that this tag is a "branch" tag, meaning that someone can check out a new tree based on this tag and do development. \\
If you omit the -b, the label will be a "sticky" tag, meaning that someone won't be able to check in new changes under that label. See the notes on Labeling and Branching |
| Check out a tree based on a label | cvs checkout -r labelname projectnameIf labelname was created as a "branch" tag, then you can check in changes without affecting anyone using the development tip. Otherwise files are considered "sticky" and changes cannot be checked in. |
| Change a file to be treated as a binary file after it's been added | cvs admin -kb filename A "binary file" won't have CVS keyword expansion performed on it. |
h3. \\

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h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on *{+}Linux systems{+}* with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your account, you will need to log in to the CVS Repository.&nbsp; You should only have to do this once in the window you are using during&nbsp;each session.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}cvs login{*}{color}\\
\\
\\

You should get the following response from the computer:

*Logging in to :pserver:*{*}{_}your_userName{_}{*}*@moonjelly.shore.mbari.org:2401/home/cvs*
*CVS password:*
\\

Enter your CVS password at the prompt.&nbsp; If you have entered the correct password you will be returned to a &nbsp;*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$*&nbsp;&nbsp;prompt.&nbsp; You are now logged in and can access project modules on the system.&nbsp; If you receive a login error from the system, re-check your password as forgotten passwords&nbsp;is the number one problem experienced by CVS users.&nbsp; If the problem persists, please contact Karen Salamy (the CVS Repository Administrator):&nbsp; salamy@mbari.org&nbsp;
\\ \\

----\\

\\

h3. CVS Command Line Usage


h3. \\

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h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on *{+}Linux systems{+}* with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your account, you will need to log in to the CVS Repository.&nbsp; You should only have to do this once in the window you are using during&nbsp;each session.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}cvs login{*}{color}\\
\\
\\

You should get the following response from the computer:

*Logging in to :pserver:*{*}{_}your_userName{_}{*}*@moonjelly.shore.mbari.org:2401/home/cvs*
*CVS password:*
\\

Enter your CVS password at the prompt.&nbsp; If you have entered the correct password you will be returned to a &nbsp;*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$*&nbsp;&nbsp;prompt.&nbsp; You are now logged in and can access project modules on the system.&nbsp; If you receive a login error from the system, re-check your password as forgotten passwords&nbsp;is the number one problem experienced by CVS users.&nbsp; If the problem persists, please contact Karen Salamy (the CVS Repository Administrator):&nbsp; salamy@mbari.org&nbsp; \\

----\\

h3. CVS Command Line Usage
\\ \\

h3. \\

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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test (see [Artisan Studio]).|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]|(/)|(/)|(/)|2.0|(x)|(/)|Java,C++|Eclipse|(/) The best by far|(/) Java,C++|(?)|After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | |Still have not gotten license issues cleared up so have not been able to test|$5500/$9625 float|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]| | | | | | | | | | | | | |
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[SmartDraw|http://www.smartdraw.com/exp/srd]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]|(/)|(/)|(x)|2.1|Yes, with MDG|(/)|C++, Java, C#, VB.Net, Visual Basic, Delphi, PHP, Python and ActionScript|Visual Studio and Eclipse|Yes, but I don't think automatically|Y|(?)|There are two pieces, Enterprise Architect(EA) and MDG Technology for SysML.  EA covers UML and MDG adds in SysML support. This one along with Borland one the Jolt award for 2006 for productivity. The EA tools did not really handle code well. Associations with multiplicity did not generate code correctly.|EA=$239,MDG=$100|
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue! Yep, I confirmed it.  You can tell the code generator what kind of collection you wish to use in the UML tool, but in SDE you cannot specify, it always uses object arrays (ouch!). So much for VP.|$1750 (no maint.)|
]]></property>
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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on *{+}Linux systems{+}* with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your account, you will need to log in to the CVS Repository.&nbsp; You should only have to do this once in the window you are using during&nbsp;each session.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}cvs login{*}{color}\\
\\
\\

You should get the following response from the computer:

*Logging in to :pserver:*{*}{_}your_userName{_}{*}*@moonjelly.shore.mbari.org:2401/home/cvs*
*CVS password:*
\\

Enter your CVS password at the prompt.&nbsp; If you have entered the correct password you will be returned to a &nbsp;*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$*&nbsp;&nbsp;prompt.&nbsp; You are now logged in and can access project modules on the system.&nbsp; If you receive a login error from the system, re-check your password as forgotten passwords&nbsp;is the number one problem experienced by CVS users.&nbsp; If the problem persists, please contact Karen Salamy (the CVS Repository Administrator):&nbsp; {color:#3300cc}salamy@mbari.org&nbsp;&nbsp;{color} {color:#000000}.{color}\\



----\\ \\ \---\-
\\

h3. CVS Command Line Usage

\\
\\

h3. \\

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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test (see [Artisan Studio]).|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]|(/)|(/)|(/)|2.0|(x)|(/)|Java,C++|Eclipse|(/) The best by far|(/) Java,C++|(?)|After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | |Still have not gotten license issues cleared up so have not been able to test|$5500/$9625 float|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]|(/)|(/)|(/)|2.1|(/)|(/)|Java/J2EE, C#, C++, CORBA IDL, .NET, XML Schema, WSDL, Database Schema, DDL Generation|(?)|Yes for Java and C++|Yes, same list as Languages|(?)| |This is a bit involved.  I figured we would want Enterprise mobile licenses as this allows on user to have it on three machines.  Todd Anderson bought two licenses in 1999, so we could upgrade them for $1906 (that is for both).  New mobile licenses are $1799 for locked and $2540 for concurrent.  We will most likely get academic pricing which takes of %40 so that would end up as $1079 each for locked and $1524 floating.  Maintence for new would also tack on $300 for each license.|
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[SmartDraw|http://www.smartdraw.com/exp/srd]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]|(/)|(/)|(x)|2.1|Yes, with MDG|(/)|C++, Java, C#, VB.Net, Visual Basic, Delphi, PHP, Python and ActionScript|Visual Studio and Eclipse|Yes, but I don't think automatically|Y|(?)|There are two pieces, Enterprise Architect(EA) and MDG Technology for SysML.  EA covers UML and MDG adds in SysML support. This one along with Borland one the Jolt award for 2006 for productivity. The EA tools did not really handle code well. Associations with multiplicity did not generate code correctly.|EA=$239,MDG=$100|
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue! Yep, I confirmed it.  You can tell the code generator what kind of collection you wish to use in the UML tool, but in SDE you cannot specify, it always uses object arrays (ouch!). So much for VP.|$1750 (no maint.)|
]]></property>
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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on *{+}Linux systems{+}* with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your account, you will need to log in to the CVS Repository.&nbsp; You should only have to do this once in the window you are using during&nbsp;each session.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}cvs login{*}{color}\\
\\
\\

You should get the following response from the computer:

*Logging in to :pserver:*{*}{_}your_userName{_}{*}*@moonjelly.shore.mbari.org:2401/home/cvs*
*CVS password:*
\\

Enter your CVS password at the prompt.&nbsp; If you have entered the correct password you will be returned to a &nbsp;*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$*&nbsp;&nbsp;prompt.&nbsp; You are now logged in and can access project modules on the system.&nbsp; If you receive a login error from the system, re-check your password as forgotten passwords&nbsp;is the number one problem experienced by CVS users.&nbsp; If the problem persists, please contact Karen Salamy (the CVS Repository Administrator):&nbsp; {color:#3300cc}salamy@mbari.org&nbsp;&nbsp;{color} {color:#000000}.{color}
\\

----
h3. {color:#000000}Logging in to CVS{color}

h3. CVS Command Line Usage

\\
\\

h3. \\

\\]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test (see [Artisan Studio]).|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]|(/)|(/)|(/)|2.0|(x)|(/)|Java,C++|Eclipse|(/) The best by far|(/) Java,C++|(?)|After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | |Still have not gotten license issues cleared up so have not been able to test|$5500/$9625 float|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]|(/)|(/)|(/)|2.1|(/)|(/)|Java/J2EE, C#, C++, CORBA IDL, .NET, XML Schema, WSDL, Database Schema, DDL Generation|(?)|Yes for Java and C++|Yes, same list as Languages|(?)| |This is a bit involved.  I figured we would want Enterprise mobile licenses as this allows on user to have it on three machines.  Todd Anderson bought two licenses in 1999, so we could upgrade them for $1906 (that is for both).  New mobile licenses are $1799 for locked and $2540 for concurrent.  We will most likely get academic pricing which takes of %40 so that would end up as $1079 each for locked and $1524 floating.  Maintence for new would also tack on $300 for each license. SysML and DODAF plugins cost extra and would be about $549 for both (each license).|
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[SmartDraw|http://www.smartdraw.com/exp/srd]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]|(/)|(/)|(x)|2.1|Yes, with MDG|(/)|C++, Java, C#, VB.Net, Visual Basic, Delphi, PHP, Python and ActionScript|Visual Studio and Eclipse|Yes, but I don't think automatically|Y|(?)|There are two pieces, Enterprise Architect(EA) and MDG Technology for SysML.  EA covers UML and MDG adds in SysML support. This one along with Borland one the Jolt award for 2006 for productivity. The EA tools did not really handle code well. Associations with multiplicity did not generate code correctly.|EA=$239,MDG=$100|
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue! Yep, I confirmed it.  You can tell the code generator what kind of collection you wish to use in the UML tool, but in SDE you cannot specify, it always uses object arrays (ouch!). So much for VP.|$1750 (no maint.)|
]]></property>
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h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit their respective websites.

Contact Kevin Gomes [mailto:kgomes@mbari.org], Brian Schlining [mailto:brian@mbari.org] or Kent Headley [mailto:headley@mbari.org] with questions or permission requests for certain tools.

{tip:title=External Availability}
Please note that Confluence, JIRA, and Alfresco are all available outside the MBARI firewall and can have external collaborator accounts that are not MBARI accounts.  This was a desirable feature of these tools and allows us to externally collaborate without risking security breaches at MBARI.
{tip}

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.
----
h3. Authentication and Single Sign On With Crowd

[Crowd|http://www.atlassian.com/crowd] is an authentication tool that is developed by [Atlassian|http://www.atlassian.com] and is provided to MBARI under a community/non-profit license.  It provides an internal user database so we can create external user accounts that can then be linked to other applications such as JIRA and Confluence.  It also connects to our internal MBARI user database using LDAP so that MBARI users can have Single Sign on capability across multiple applications.

Links for Crowd at MBARI:
* [Crowd Web Application|http://oceana.mbari.org:8095/crowd]
* [Documentation of MBARI Crowd Installation|SPEPRJ:MBARI Crowd Installation]

----
h3. Content Management with [Alfresco|https://alfresco.mbari.org/alfresco]

Alfresco is a Content Management System (CMS) intended to replace the Project Library on Tornado as the repository for MBARI project documentation. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

{info:title=Accounting Creates Projects in Alfresco}
One of the main benefits of Alfresco is that it can interact with our accounting system in an automated fashion. Because of this, we have the accounting system currently creating project spaces and directory structures in Alfresco automatically.  This allows the accounting software to then export all accounting activity (PDFs of AMEX, PO's, etc.) to the Alfresco spaces automatically.
{info}

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password without using "shore\" in front) to see the project library materials. The *Projects* folder is the space that contains the content for projects at MBARI.

To create a short cut to the Projects folder (or any folder), enter that folder, then select "More Actions/View Details", then "Create Shortcut" (on the right side of the page).  This will create a shortcut that will be available in the "Shelf".  To view the shortcuts in your "Shelf", click on the down arrow next to "Navigtor" on the left hand sidebar menu, then select "Shelf" and you will see your created shortcuts.

Here are some useful links related to MBARI's installation of Alfresco:
* [Alfresco's Homepage|http://www.alfresco.com/]
* [Alfresco's Developer Home Page|http://wiki.alfresco.com/wiki/Main_Page]
* [Alfresco's Enterprise Customer Portal|https://network.alfresco.com/extranet/]
* [Deployment Information for MBARI's Alfresco Installation|Deployment Information]
* [Installation Notes]
* [alfresco.mbari.org Installation Notes]
* [alfresco-test.shore.mbari.org Installation Notes]

----
h3. WIKI Collaboration Pages ([Confluence|https://oceana.mbari.org/confluence])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

# [SPEPRJ:Confluence Installation Notes]

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts an externally accessable Maven repository at [https://oceana.mbari.org/maven2], an internal repository at [http://seaspray.shore.mbari.org:8082/archiva/repository/internal/] and a repository manager at [http://seaspray.shore.mbari.org:8082/archiva]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [SPEPRJ:Maven At MBARI] for more details.

h3. Modeling with UML (JBuilder 2008 R2)

You can download JBuilder 2008 R2 from here:

[Mac OS X|http://altd.embarcadero.com/download/jbuilder/JBuilder_2008R2/jbuilder2008r2.macosx.tar.gz]
[Linux|http://altd.embarcadero.com/download/jbuilder/JBuilder_2008R2/jbuilder2008r2.linux.tar.gz]
[Windows|http://altd.embarcadero.com/download/jbuilder/JBuilder_2008R2/jbuilder2008r2.win32.zip]

Once downloaded and installed, you need to copy the following [.slip|https://alfresco.mbari.org/alfresco/webdav/Engineering/Tools/Collaboration%20Tools/JBuilder/concurrent_48444.slip] file to the:

JBUILDER_HOME/license

directory.

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on *{+}Linux systems{+}* with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your account, you will need to log in to the CVS Repository.&nbsp; You should only have to do this once in the window you are using during the session.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}cvs login{*}{color}\\
\\
\\

You should get the following response from the computer:

*Logging in to :pserver:*{*}{_}your_userName{_}{*}*@moonjelly.shore.mbari.org:2401/home/cvs*
*CVS password:*
\\

Enter your CVS password at the prompt.&nbsp; If you have entered the correct password you will be returned to a *\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* prompt.&nbsp; You are now logged in and can access project modules on the system.&nbsp; If you receive a login error from the system, re-check your password as it is the number one problem experienced by CVS users.&nbsp; If the problem persists, please contact Karen Salamy (the CVS Repository Administrator):&nbsp; salamy@mbari.org&nbsp;
\\

----\\

h3. CVS Command Line Usage


h3. \\
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h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on *{+}Linux systems{+}* with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your account, you will need to log in to the CVS Repository.&nbsp; You should only have to do this once in the window you are using during&nbsp;each session.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}cvs login{*}{color}\\
\\
\\

You should get the following response from the computer:

*Logging in to :pserver:*{*}{_}your_userName{_}{*}*@moonjelly.shore.mbari.org:2401/home/cvs*
*CVS password:*
\\

Enter your CVS password at the prompt.&nbsp; If you have entered the correct password you will be returned to a &nbsp;*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$*&nbsp;&nbsp;prompt.&nbsp; You are now logged in and can access project modules on the system.&nbsp; If you receive a login error from the system, re-check your password as forgotten passwords&nbsp;is the number one problem experienced by CVS users.&nbsp; If the problem persists, please contact Karen Salamy (the CVS Repository Administrator):&nbsp; salamy@mbari.org&nbsp;
\\

\---\-
\\

h3. CVS Command Line Usage


h3. \\

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h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit their respective websites.

Contact Kevin Gomes [mailto:kgomes@mbari.org], Brian Schlining [mailto:brian@mbari.org] or Kent Headley [mailto:headley@mbari.org] with questions or permission requests for certain tools.

{tip:title=External Availability}
Please note that Confluence, JIRA, and Alfresco are all available outside the MBARI firewall and can have external collaborator accounts that are not MBARI accounts.  This was a desirable feature of these tools and allows us to externally collaborate without risking security breaches at MBARI.
{tip}

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.
----
h3. Authentication and Single Sign On With Crowd

[Crowd|http://www.atlassian.com/crowd] is an authentication tool that is developed by [Atlassian|http://www.atlassian.com] and is provided to MBARI under a community/non-profit license.  It provides an internal user database so we can create external user accounts that can then be linked to other applications such as JIRA and Confluence.  It also connects to our internal MBARI user database using LDAP so that MBARI users can have Single Sign on capability across multiple applications.

Links for Crowd at MBARI:
* [Crowd Web Application|http://oceana.mbari.org:8095/crowd]
* [Documentation of MBARI Crowd Installation|SPEPRJ:MBARI Crowd Installation]

----
h3. Content Management with [Alfresco|https://alfresco.mbari.org/alfresco]

Alfresco is a Content Management System (CMS) intended to replace the Project Library on Tornado as the repository for MBARI project documentation. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

{info:title=Accounting Creates Projects in Alfresco}
One of the main benefits of Alfresco is that it can interact with our accounting system in an automated fashion. Because of this, we have the accounting system currently creating project spaces and directory structures in Alfresco automatically.  This allows the accounting software to then export all accounting activity (PDFs of AMEX, PO's, etc.) to the Alfresco spaces automatically.
{info}

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password without using "shore\" in front) to see the project library materials. The *Projects* folder is the space that contains the content for projects at MBARI.

To create a short cut to the Projects folder (or any folder), enter that folder, then select "More Actions/View Details", then "Create Shortcut" (on the right side of the page).  This will create a shortcut that will be available in the "Shelf".  To view the shortcuts in your "Shelf", click on the down arrow next to "Navigtor" on the left hand sidebar menu, then select "Shelf" and you will see your created shortcuts.

Here are some useful links related to MBARI's installation of Alfresco:
* [Alfresco's Homepage|http://www.alfresco.com/]
* [Alfresco's Developer Home Page|http://wiki.alfresco.com/wiki/Main_Page]
* [Alfresco's Enterprise Customer Portal|https://network.alfresco.com/extranet/]
* [Deployment Information for MBARI's Alfresco Installation|Deployment Information]
* [Installation Notes]
* [SPEPRJ:alfresco.mbari.org Installation Notes]
* [alfresco-test.shore.mbari.org Installation Notes]

----
h3. WIKI Collaboration Pages ([Confluence|https://oceana.mbari.org/confluence])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

# [SPEPRJ:Confluence Installation Notes]

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts an externally accessable Maven repository at [https://oceana.mbari.org/maven2], an internal repository at [http://seaspray.shore.mbari.org:8082/archiva/repository/internal/] and a repository manager at [http://seaspray.shore.mbari.org:8082/archiva]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [SPEPRJ:Maven At MBARI] for more details.

h3. Modeling with UML (JBuilder 2008 R2)

You can download JBuilder 2008 R2 from here:

[Mac OS X|http://altd.embarcadero.com/download/jbuilder/JBuilder_2008R2/jbuilder2008r2.macosx.tar.gz]
[Linux|http://altd.embarcadero.com/download/jbuilder/JBuilder_2008R2/jbuilder2008r2.linux.tar.gz]
[Windows|http://altd.embarcadero.com/download/jbuilder/JBuilder_2008R2/jbuilder2008r2.win32.zip]

Once downloaded and installed, you need to copy the following [.slip|https://alfresco.mbari.org/alfresco/webdav/Engineering/Tools/Collaboration%20Tools/JBuilder/concurrent_48444.slip] file to the:

JBUILDER_HOME/license

directory.

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on *{+}Linux systems{+}* with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your account, you will need to log in to the CVS Repository.&nbsp; You should only have to do this once in the window you are using during&nbsp;each session.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}cvs login{*}{color}\\
\\
\\

You should get the following response from the computer:

*Logging in to :pserver:*{*}{_}your_userName{_}{*}*@moonjelly.shore.mbari.org:2401/home/cvs*
*CVS password:*
\\

Enter your CVS password at the prompt.&nbsp; If you have entered the correct password you will be returned to a &nbsp;*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$*&nbsp;&nbsp;prompt.&nbsp; You are now logged in and can access project modules on the system.&nbsp; If you receive a login error from the system, re-check your password as forgotten passwords&nbsp;is the number one problem experienced by CVS users.&nbsp; If the problem persists, please contact Karen Salamy (the CVS Repository Administrator):&nbsp; {color:#3300cc}salamy@mbari.org{color}&nbsp;
\\

\---\-
\\

h3. CVS Command Line Usage


h3. \\

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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-6.5.8.zip|^smartsvn-windows-x86-setup-nojre-6_5_8.zip|SmartSVN for Windows version 6.5.8]&nbsp;&nbsp; {color:#ff0000}*\- NEW\!*{color}

\\
\\
\\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-Mac-6.5.8.tar.gz|^smartsvn-macosx-6_5_8.tar.gz|SmartSVN Macintosh version 6.5.8]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}

\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-Linux-6.5.8.tar.gz|^smartsvn-generic-6_5_8.tar.gz|SmartSVN Linux version 6.5.8]&nbsp;{color:#ff0000}*\- NEW\!*{color}

\\
\\
\\
\\
\\
\\
\\
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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your account, you will need to log in to the CVS Repository.&nbsp; You should only have to do this once in the window you are using during the session.\\

*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}cvs login{*}{color}\\ \\

\\
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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your account, you will need to log in to the CVS Repository.&nbsp; You should only have to do this once in the window you are using during the session.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}cvs login{*}{color}\\
\\

\\
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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your account, you will need to log in to the CVS Repository.&nbsp; You should only have to do this once in the window you are using during the session.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}cvs login{*}{color}\\
\\ \\

You should get the following response from the computer:

*Logging in to :pserver:*{*}{_}your_userName{_}{*}*@moonjelly.shore.mbari.org:2401/home/cvs*
*CVS password:*\\

Enter your CVS password at the prompt.&nbsp; If you have entered the correct password you will be returned to a *\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* prompt.&nbsp; You are now logged in and can access project modules on the system.&nbsp; If you receive a login error from the system, re-check your password as it is the number one problem experienced by CVS users.&nbsp; If the problem persists, please contact Karen Salamy (the CVS Repository Administrator):&nbsp; salamy@mbari.org&nbsp;\\

----
&nbsp;

h3. CVS Command Line Usage


h3. \\
&nbsp;]]></property>
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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.\\

{color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.
\\

*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your accout

\\
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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file:\\

{color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.\\

*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your accout

\\
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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file.

\\ {color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}

\\
This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

{color:#ff0000}{*}NOTE\!\!*{color} Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\\
*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}

\\

----
h3. Logging in to CVS

\\

After logging into your accout

\\
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# ADCP: Acoustic Doppler Current Profiler - a sonar that attempts to produce a record of water current velocities for a range of depths [http://en.wikipedia.org/wiki/Acoustic_Doppler_Current_Profiler]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AMQP: Advanced Message Queuing Protocol - [http://www.amqp.org]
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ARI-WG: Access to Remote Instrumentation in a distributed environment - Working Group. OpenGrid Forum [http://www.ogf.org/gf/group_info/view.php?group=ari-wg]
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EarthCube: EarthCube is a NSF activity to create a data and knowledge management system for the 21st Century. The scientific objective is to develop a framework over the next decade to understand and predict the Earth system from the sun to the center of the Earth [http://earthcube.ning.com/]
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GNB: Gaussian Naïve Bayes. GNB is a probabilistic classifier relying on Bayes rule to estimate posterior probabilities of labels given the data. Naive assumption in it is an independence of the features. See http://en.wikipedia.org/wiki/Naive_bayes for more information. 
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# HDF: Hierarchical Data Format
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# JVM: Java Virtual Machine - [http://en.wikipedia.org/wiki/Jvm]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MB/CA Current: a MBARI project in 2011
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MODIS: Moderate Resolution Imaging Spectroradiometer is a key instrument aboard the Terra (EOS AM) and Aqua (EOS PM) satellites.
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NODC: National Oceanographic Data Center - http://www.nodc.noaa.gov/
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# ODSS: Oceanographic Decision Support System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOI CI: Ocean Observatories Initiative CyberInfrastructure: [http://ci.oceanobservatories.org/] (Developers site: [http://ooici.net/])
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software).
# SCPI: Self Contained Plankton Imager, an MBARI project in 2011
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WCS: Web Coverage Service
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file:

{color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}
\\
\\

This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

\[_userName_@_computerName_\]$ *source \~/.bashrc*\\
\\

----
h3. Logging in to CVS

\\

After logging into your accout

\\
\\]]></property>
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<property name="body"><![CDATA[h2.


----
h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

\\
&nbsp;

[SVN Client Software Downloads|CLT:SVN Client Software Downloads] {color:#ff0000}\- Windows, Macs, Linux Systems{color}

[Setting up SVN Client&nbsp;to MBARI SVN Repository|CLT:Setting up SmartSVN]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository] {color:#ff0000}\- Non&nbsp;SVN client&nbsp;method{color}

[View the SVN Repository|http://kahuna.shore.mbari.org/viewvc/?root=svn]

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&nbsp;
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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file:

{color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_username{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}
\\
\\

This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.
\\
\\
\\

----
h3. Logging in to CVS
\\

After logging into your accout

\\
\\]]></property>
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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file:

{color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_userName{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}
\\
\\

This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).

Remember to re-source your .bashrc file the first time you set this up so that the edit takes effect.

*\[*{*}{_}userName{_}{*}*@*{*}{_}computerName{_}{*}*\]$* {color:#3300cc}{*}source \~/.bashrc{*}{color}\\
\\

----
h3. Logging in to CVS

\\

After logging into your accout

\\
\\]]></property>
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<id name="id">8388646</id>
<property name="body"><![CDATA[h2.


----
h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.&nbsp; To gain access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; {color:#ff0033}{*}NOTE:*{color} {color:#ff0033}In the rare event the administrator is on vacation or unavailable, please&nbsp;submit your&nbsp;SVN request to the IS Remedy page at:&nbsp;{color} https://ishelp.shore.mbari.org/helpdesk/WebObjects/Helpdesk {color:#ff0033}and it will be assigned by IS appropriately based on urgency level.{color}

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

\\
&nbsp;

[SVN Client Software Downloads|CLT:SVN Client Software Downloads] {color:#ff0000}\- Windows, Macs, Linux Systems{color}

[Setting up SVN Client&nbsp;to MBARI SVN Repository|CLT:Setting up SmartSVN]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository] {color:#ff0000}\- Non&nbsp;SVN client&nbsp;method{color}

[View the SVN Repository|http://kahuna.shore.mbari.org/viewvc/?root=svn]

\\
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&nbsp;
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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file:

{color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_username{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}
\\ \\

This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).
\\
\\
\\
\\
\\]]></property>
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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file:

{color:#3300cc}{*}export CVSROOT=:pserver:*{color}{color:#3300cc}{*}{_}your_username{_}{*}{color}{color:#3300cc}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}
\\
\\

This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).
\\
\\
\\

----
h3. Logging in to CVS

\\
\\]]></property>
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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user /home account and&nbsp;add the following line to&nbsp;your account's .bashrc file:


*export CVSROOT=:pserver:*{*}{_}your_username{_}{*}*@moonjelly.shore.mbari.org:/home/cvs*
\\
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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user */home* account and&nbsp;add the following line to&nbsp;your account's *.bashrc* file:

{color:#ff0000}{*}export CVSROOT=:pserver:*{color}{color:#ff0000}{*}{_}your_username{_}{*}{color}{color:#ff0000}*@moonjelly.shore.mbari.org:/home/cvs{*}{color}
\\
\\

This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).
\\
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h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user /home account and&nbsp;add the following line to&nbsp;your account's .bashrc file:\\

*export CVSROOT=:pserver:*{*}{_}your_username{_}{*}*@moonjelly.shore.mbari.org:/home/cvs*
\\
\\

This will allow you to access the CVS Repository without having to set up the CVSROOT each time (i.e.,&nbsp;your CVSROOT will be renewed each time you log in to your computer).
\\
\\
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h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.

----\\ To set up the CVSROOT on your Linux system, first log into your user /home account on your machine and&nbsp;add the following line to&nbsp;your account's .bashrc file:

*export CVSROOT=:pserver:*{*}{_}your_username{_}{*}*@moonjelly.shore.mbari.org:/home/cvs*
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h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.

----\\
To set up the CVSROOT on your Linux system, first log into your user /home account on your machine and&nbsp;add the following line to&nbsp;your account's .bashrc file:
*export CVSROOT=:pserver:*{*}{_}your_username{_}{*}*@moonjelly.shore.mbari.org:/home/cvs*
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h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.\\

To set up the CVSROOT on your Linux system, first log into your user /home account on your machine and&nbsp;add the following line to&nbsp;your account's .bashrc file:

*export CVSROOT=:pserver:*{*}{_}your_username{_}{*}*@moonjelly.shore.mbari.org:/home/cvs*\\]]></property>
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h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.

----
h3. Setup of .bashrc file

\\
To set up the CVSROOT on your Linux system, first log into your user /home account on your machine and&nbsp;add the following line to&nbsp;your account's .bashrc file:
*export CVSROOT=:pserver:*{*}{_}your_username{_}{*}*@moonjelly.shore.mbari.org:/home/cvs*
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<property name="body"><![CDATA[----
h3. Command Line Access Setup

The MBARI CVS Repository may be accessed&nbsp;on Linux systems with&nbsp;Command Line control should you decide to not use a GUI.

----
\\
To set up the CVSROOT on your Linux system, first log into your user /home account on your machine and&nbsp;add the following line to&nbsp;your account's .bashrc file:
*export CVSROOT=:pserver:*{*}{_}your_username{_}{*}*@moonjelly.shore.mbari.org:/home/cvs*
\\
\\
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[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

[*Setup to access CVS Repository with Command line instead of GUI (Linux users)*|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)]\\ \\

----]]></property>
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[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

[*Setup to access CVS Repository with Command line instead of GUI (Linux users)*|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)]\\ \\

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&nbsp;

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----
[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

Setup to access CVS Repository with Command line instead of GUI (Linux users)]]></property>
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----

\\
&nbsp;

[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

[*Setup to access CVS Repository with Command line instead of GUI (Linux users)*|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)]\\
\\

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&nbsp;

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----\\ \\

[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

[*Setup to access CVS Repository with Command line instead of GUI (Linux users)*|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)]\\
\\

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&nbsp;

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----

\\
\\
&nbsp;

[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

[*Setup to access CVS Repository with Command line instead of GUI (Linux users)*|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)]\\
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&nbsp;

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----
*[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21]*

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator (_Karen Salamy:&nbsp;_ salamy@mbari.org). Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see:_ [Seeting up a CVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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----
*[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21]*

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator (_Karen Salamy:&nbsp;_ salamy@mbari.org). Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see:_ [Seeting up a CVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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----
[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

Setup to access CVS Repository with Command line instead of GUI (Linux users)

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator (_Karen Salamy:&nbsp;_ salamy@mbari.org). Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see:_ [Seeting up a CVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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<property name="body"><![CDATA[h2.


----
[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator (_Karen Salamy:&nbsp;_ salamy@mbari.org). Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see:_ [Seeting up a CVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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----


h2. Standard method of operation for working with the CVS GUI clients
\\

\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator (_Karen Salamy:&nbsp;_ salamy@mbari.org). Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see:_ [Seeting up a CVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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----Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator (_Karen Salamy:&nbsp;_ salamy@mbari.org). Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see:_ [Seeting up a CVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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----


h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator (_Karen Salamy:&nbsp;_ salamy@mbari.org). Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see:_ [Seeting up a CVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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----
*[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21]*

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

*[*Adding code to CVS Repository with WinCVS GUI*|CLT:Adding code to CVS Repository with WinCVS GUI]*

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator (_Karen Salamy:&nbsp;_ salamy@mbari.org). Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see:_ [Seeting up a CVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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----
*[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21]*

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator (_Karen Salamy:&nbsp;_ salamy@mbari.org). Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see:_ [Seeting up a CVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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----
h2. Standard method of operation for working with the CVS GUI clients


h6.

{color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator (_Karen Salamy:&nbsp;_ salamy@mbari.org). Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see:_ [Seeting up a CVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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----
h2. Standard method of operation for working with the CVS GUI clients

{color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator (_Karen Salamy:&nbsp;_ salamy@mbari.org). Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see:_ [Seeting up a CVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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<property name="body"><![CDATA[----
h3. *Setting up WinCVS (v. 1.2) on your Windows 2000/XP (x86) computer to access the MBARI&nbsp;*{*}{_}moonjelly{_}* *CVS source code repository.*&nbsp;

*1).* To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[https://oceana.mbari.org/confluence/display/~salamy/Helpful+Software+Downloads] and copy&nbsp;the *{_}WinCVS-1.2.0.zip{_}* folder to your Desktop.&nbsp; Extract all files to your *{_}C:\Program_Files{_}*&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
*2).* Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as *{_}C:\Program_Files\GNU\WinCVS_1.2{_}* .

\\
*3).*&nbsp;Once installed, open WinCVS (*{_}Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS{_}*).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says *"ENTER THE CVSROOT"* .&nbsp; An example of this would be (_salamy@moonjelly:/home/cvs_) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the *"AUTHENTIFICATION:"* setting to - *_"passwd" file on the cvs server._*
* Finally, click the _WinCVS_ tab and set your *"home"* directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).
\\

\\
*&nbsp;4).*&nbsp;*NOTE:*&nbsp; To actually use this GUI on the moonjelly repository you will first need an excrypted CVS respository password (see also&nbsp;*"Password Access"* at the following link: [https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21]
* To do this, telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command {color:#ff0000}{*}{+}encryptCVSpw{+}{*}{color}.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (\*_exactly as listed_\*) to the CVS&nbsp;administrator (*salamy@mbari.org). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
A good way to maneuver through the repository with your GUI is to have your web browser open to: http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/ the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.
\\
\\
\\

*5).*&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AMQP: Advanced Message Queuing Protocol - http://www.amqp.org
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ARI-WG: Access to Remote Instrumentation in a distributed environment - Working Group. OpenGrid Forum [http://www.ogf.org/gf/group_info/view.php?group=ari-wg]
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MB/CA Current: a MBARI project in 2011
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOI CI: Ocean Observatories Initiative CyberInfrastructure: [http://ci.oceanobservatories.org/] (Developers site: [http://ooici.net/])
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software).
# SCPI: Self Contained Plankton Imager, an MBARI project in 2011
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator (_Karen Salamy:&nbsp;_ salamy@mbari.org). Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see:_ [Seeting up a CVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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<property name="body"><![CDATA[h3.


----
h3. Download and Install Client&nbsp;

To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
To set up the SmartSVN client, run the application.&nbsp; Next, choose "*Project"* from the&nbsp;Main Menu and then click on "*Check Out..."*

This should bring you to the following page:

\\ !Screen_Save_Checkout_small.jpg|align=left!\\
\\
\\

Click on the&nbsp;*"Manage"* button, create&nbsp;and edit a new profile called&nbsp;*"MBARI_SVN"*&nbsp;as follows:

\\ !Screen_Saver_Edit_Repo_small.jpg|align=left!\\
\\

{color:#ff0000}{*}NOTE:\!\!&nbsp;*{color} Make sure you use your own personal *Login Name* when creating this profile and check that the *"Verify connection when pressing 'OK'"* box is clicked in order to verify that your computer is able to connect with the SVN server kahuna.
\\
\\

\\
\\
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<property name="body"><![CDATA[h3.


----
h3. Download and Install Client&nbsp;

To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
To set up the SmartSVN client, run the application.&nbsp; Next, choose "*Project"* from the&nbsp;Main Menu and then click on "*Check Out..."*

This should bring you to the following page:

\\ !Screen_Save_Checkout_small.jpg|align=left!\\
\\
\\

Click on the&nbsp;*"Manage"* button, create&nbsp;and edit a new profile called&nbsp;*"MBARI_SVN"*&nbsp;as follows:

\\ !Screen_Saver_Edit_Repo_small.jpg|align=left!\\
\\ {color:#ff0000}{*}NOTE\!\!&nbsp;*{color} Make sure you use your own personal *Login Name* when creating this profile and check that the *"Verify connection when pressing 'OK'"* box is clicked in order to verify that your computer is able to connect with the SVN server kahuna.
\\
\\
\\
\\
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<property name="body"><![CDATA[----
h3. *{+}Welcome to CVS\!+*

CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp;&nbsp;Someone has&nbsp;requested that you be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

h3. \\


h3. +Permissions+

Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. _moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot access _moonjelly_ for any reason, please let me know.

\\
&nbsp;

h3. +Password Access+

Access to the repository requires another (_separate_) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network (_usually with the command prompt, Cygwin Window, or a Linux Terminal_), telnet and login to _moonjelly_ with your standard MBARI password and type the following at the prompt: &nbsp;{color:red}{*}encryptCVSpw{*}{color}
This runs a script that outputs an encrypted version of your password.&nbsp; You may put any password in that you wish - even the same one as your standard MBARI network password.&nbsp; That is up to you.

Next, *{+}Please e-mail me the encrypted text (exactly as shown)+* so that I may add you to the repository password list.&nbsp; I will send you an e-mail when you are able to access the repository.

\\
&nbsp;

h3. *{+}CVS GUIs{+}*

GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the link [Setting up WinCVS_1.2|CLT:CVS Client Software Downloads^Setting up WinCVS_1.2_new.doc]. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. Please&nbsp;remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

Regards, - Karen A. Salamy (_MBARI CVS administrator)_ \- salamy@mbari.org
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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----
h3. Download and Install Client&nbsp;

To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
To set up the SmartSVN client, run the application.&nbsp; Next, choose "*Project"* from the&nbsp;Main Menu and then click on "*Check Out..."*

This should bring you to the following page:

\\ !Screen_Save_Checkout_small.jpg|align=left!\\
\\

\\
&nbsp; ]]></property>
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----
h3. Download and Install Client&nbsp;

To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
To set up the SmartSVN client, run the application.&nbsp; Next, choose "*Project"* from the&nbsp;Main Menu and then click on "*Check Out..."*

This should bring you to the following page:

\\ !Screen_Save_Checkout_small.jpg|align=left!\\
\\
\\

Click on the&nbsp;*"Manage"* button, create&nbsp;and edit a new profile called&nbsp;*"MBARI_SVN"*&nbsp;as follows:
\\ !Screen_Saver_Edit_Repo_small.jpg|align=left!\\
\\
\\
\\]]></property>
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<property name="body"><![CDATA[h3.


----
h3. Download and Install Client&nbsp;

To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
To set up the SmartSVN client, run the application.&nbsp; Next, choose "*Project"* from the&nbsp;Main Menu and then click on "*Check Out..."*

This should bring you to the following page:

\\ !Screen_Save_Checkout_small.jpg|align=left!\\
\\ \\

Click on the&nbsp;*"Manage"* button, create&nbsp;and edit a new profile called&nbsp;"*MBARI_SVN"&nbsp;*as follows:\\ !Screen_Saver_Edit_Repo_small.jpg|align=left!\\ \\ \\ \\]]></property>
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<property name="body"><![CDATA[h3.


----
h3. Download and Install Client&nbsp;

To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
To set up the SmartSVN client, run the application.&nbsp; Next, choose "*Project"* from the&nbsp;Main Menu and then click on "*Check Out..."*

This should bring you to the following page:

\\ !Screen_Save_Checkout_small.jpg|align=left!\\
\\
\\

Click on the&nbsp;*"Manage"* button, create&nbsp;and edit a new profile called&nbsp;*"MBARI_SVN"*&nbsp;as follows:

\\ !Screen_Saver_Edit_Repo_small.jpg|align=left!\\
\\
\\
\\]]></property>
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<property name="body"><![CDATA[h3.


----
h3. Download and Install Client&nbsp;

To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
To set up the SmartSVN client, run the application.&nbsp; Next, choose "*Project"* from the&nbsp;Main Menu and then click on "*Check Out..."*

This should bring you to the following page:

\\ !Screen_Save_Checkout_small.jpg|align=left!\\
\\
\\

Click on the&nbsp;*"Manage"* button, create&nbsp;and edit a new profile called&nbsp;*"MBARI_SVN"*&nbsp;as follows:

\\ !Screen_Saver_Edit_Repo_small.jpg|align=left!\\
\\

Make sure you use your own personal *Login Name* when creating this profile and check that the *"Verify connection when pressing 'OK'"* box is clicked in order to verify that your computer is able to connect with the SVN server kahuna.\\ \\

\\
\\
&nbsp;]]></property>
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<property name="body"><![CDATA[h3. Download and Install Client&nbsp;

To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
To set up the SmartSVN client, run the application.&nbsp; Next, choose *Project* from the top menu and then click on *Check Out...* This should bring you to the following page:

\\
&nbsp;]]></property>
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To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
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<property name="body"><![CDATA[h3. Download and Install Client&nbsp;

To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
To set up the SmartSVN client, run the application.&nbsp; Next, choose *Project* from the top menu and then click on *Check Out...* This should bring you to the following page:

\\
&nbsp; ]]></property>
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<property name="body"><![CDATA[h3. Download and Install Client&nbsp;

To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
To set up the SmartSVN client, run the application.&nbsp; Next, choose *Project* from the top menu and then click on *Check Out...* This should bring you to the following page:

\\
&nbsp; !Screen_Save_Checkout.jpg|align=left!]]></property>
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<property name="body"><![CDATA[h3. Download and Install Client&nbsp;

To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
To set up the SmartSVN client, run the application.&nbsp; Next, choose *Project* from the top menu and then click on *Check Out...* This should bring you to the following page: !Screen_Save_Checkout_small.jpg|align=left!
\\
&nbsp; ]]></property>
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----


h3. Download and Install Client&nbsp;

To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
To set up the SmartSVN client, run the application.&nbsp; Next, choose *Project* from the top menu and then click on *Check Out...*

This should bring you to the following page:

\\ !Screen_Save_Checkout_small.jpg|align=left!\\
\\

\\
&nbsp; ]]></property>
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To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
To set up the SmartSVN client, run the application.&nbsp; Next, choose *Project* from the top menu and then click on *Check Out...* This should bring you to the following page: \\ !Screen_Save_Checkout_small.jpg|align=left!\\ \\

\\
&nbsp; ]]></property>
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<property name="body"><![CDATA[h3. Introduction
This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org:8082/].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h3. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h4. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select 
More Actions/View Details, then "Create Shortcut" (on the right side fo the page). 

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h4. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h4. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h4. Modelling with UML (Together)

After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

MBARI SDS has purchased several Together floating licenses. Contact Kevin Gomes for information on using this tool.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.  

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<property name="body"><![CDATA[h3. Introduction
This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org:8082/].

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h4. Content Management Tool ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select 
More Actions/View Details, then "Create Shortcut" (on the right side fo the page). 

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h4. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h4. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h4. Modelling with UML (Together)

After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

MBARI SDS has purchased several Together floating licenses. Contact Kevin Gomes for information on using this tool.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.  

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<property name="body"><![CDATA[h3. Introduction
This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to pages with details about each specific tool.

* Content Management Tool (Alfresco)
* WIKI Collaboration Pages (Confluence)
* Issue (bug) tracking (JIRA)
* UML (?)

Here are some links to pages describing the various tools available and information about why we chose the ones we chose.  

* Content Management Tools
* WIKI Tools
* Issue Bug Trackers
* [UML]
]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[h3. Introduction
This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h3. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h4. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select 
More Actions/View Details, then "Create Shortcut" (on the right side fo the page). 

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h4. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h4. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h4. Modelling with UML (Together)

After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

MBARI SDS has purchased several Together floating licenses. Contact Kevin Gomes for information on using this tool.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.  

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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. http://www.noaa.gov
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10356117</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">11272820</id>
<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

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h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.3.zip|^smartsvn-win32-setup-nojre-4_0_3.zip]
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]
* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|^SmartSVN.zip]
\\ \\

----
h3. Macintosh

{color:#000000}({color}{color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color}{color:#000000}){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

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h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.3.zip|^smartsvn-win32-setup-nojre-4_0_3.zip]
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]
* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|^SmartSVN.zip] \\ \\

----
h3. Macintosh

{color:#000000}({color}{color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color}{color:#000000}){color}
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* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.3.zip|^smartsvn-win32-setup-nojre-4_0_3.zip]
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]
* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|^SmartSVN.zip]
\\

\\

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h3. Macintosh

{color:#000000}({color}{color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color}{color:#000000}){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
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----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
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----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})

SmartSVN-4.0.3.zip

SmartSVN-3.0.9.zip

SmartSVN-3.0.7.zip

SmartSVN-3.0.4.zip

\\
\\
&nbsp;

----
h3. Macintosh

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
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----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
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----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* {color:#000000}SmartSVN-4.0.3.zip{color}
* {color:#000000}[{color:#000000}SmartSVN-3.0.9.zip{color}|^smartsvn-win32-setup-nojre-3_0_9.zip]{color}
* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|^SmartSVN.zip]

\\
\\
&nbsp;

----
h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color}{color:#000000}){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
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----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
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----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* SmartSVN-4.0.3.zip
* SmartSVN-3.0.9.zip
* SmartSVN-3.0.7.zip
* SmartSVN-3.0.4.zip\\

----
h3. Macintosh

{color:#000000}({color}{color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color}{color:#000000}){color}
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* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
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h3. Linux

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* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool list at [http://www.softdevtools.com]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Win||LINUX||Mac||Version Tested||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
| | | | | | | | | | | | | |
||[Altova UModel|http://www.altova.com/products/umodel/uml_tool.html]|(/)|(x)|(x)|2.2|(x)|(/)|Java,C#,VB.Net|None|(/)|(/)|Windows|The windows only thing is a big issue.|$189|
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test (see [Artisan Studio]).|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]|(/)|(/)|(/)|2.0|(x)|(/)|Java,C++|Eclipse|(/) The best by far|(/) Java,C++|(?)|After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | |Still have not gotten license issues cleared up so have not been able to test|$5500/$9625 float|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]|(/)|(/)|(/)|2.1|(/)|(/)|Java/J2EE, C#, C++, CORBA IDL, .NET, XML Schema, WSDL, Database Schema, DDL Generation|(?)|Yes for Java and C++|Yes, same list as Languages|(?)|I got it up and running.  It does not generate all the clean of HTML and I could not get the roundtrip engineering to work very well.  The option to refresh the code set was greyed out so I could not synch up the code.  After laboring through it, I think I had it setup to do the code round-trip, but when I ran it, most of the classes in my diagrams disappeared and all the buttons and windows in the different panes disappeared (this could just be a Mac thing, but ouch!).  I also could not find an easy way to define associations and have them link to getter methods in the code.|This is a bit involved.  I figured we would want Enterprise mobile licenses as this allows on user to have it on three machines.  Todd Anderson bought two licenses in 1999, so we could upgrade them for $1906 (that is for both).  New mobile licenses are $1799 for locked and $2540 for concurrent.  We will most likely get academic pricing which takes of %40 so that would end up as $1079 each for locked and $1524 floating.  Maintence for new would also tack on $300 for each license. SysML and DODAF plugins cost extra and would be about $549 for both (each license).|
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[SmartDraw|http://www.smartdraw.com/exp/srd]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]|(/)|(/)|(x)|2.1|Yes, with MDG|(/)|C++, Java, C#, VB.Net, Visual Basic, Delphi, PHP, Python and ActionScript|Visual Studio and Eclipse|Yes, but I don't think automatically|Y|(?)|There are two pieces, Enterprise Architect(EA) and MDG Technology for SysML.  EA covers UML and MDG adds in SysML support. This one along with Borland one the Jolt award for 2006 for productivity. The EA tools did not really handle code well. Associations with multiplicity did not generate code correctly.|EA=$239,MDG=$100|
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue! Yep, I confirmed it.  You can tell the code generator what kind of collection you wish to use in the UML tool, but in SDE you cannot specify, it always uses object arrays (ouch!). So much for VP.|$1750 (no maint.)|
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool list at [http://www.softdevtools.com]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Altova UModel|http://www.altova.com/products/umodel/uml_tool.html]|(/)|(x)|(x)|2.2|(x)|(/)|Java,C#,VB.Net|None|(/)|(/)|Windows|The windows only thing is a big issue.|$189|
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test (see [Artisan Studio]).|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]|(/)|(/)|(/)|2.0|(x)|(/)|Java,C++|Eclipse|(/) The best by far|(/) Java,C++|(?)|After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | |Still have not gotten license issues cleared up so have not been able to test|$5500/$9625 float|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]|(/)|(/)|(/)|2.1|(/)|(/)|Java/J2EE, C#, C++, CORBA IDL, .NET, XML Schema, WSDL, Database Schema, DDL Generation|(?)|Yes for Java and C++|Yes, same list as Languages|(?)|I got it up and running.  It does not generate all the clean of HTML and I could not get the roundtrip engineering to work very well.  The option to refresh the code set was greyed out so I could not synch up the code.  After laboring through it, I think I had it setup to do the code round-trip, but when I ran it, most of the classes in my diagrams disappeared and all the buttons and windows in the different panes disappeared (this could just be a Mac thing, but ouch!).  I also could not find an easy way to define associations and have them link to getter methods in the code.|This is a bit involved.  I figured we would want Enterprise mobile licenses as this allows on user to have it on three machines.  Todd Anderson bought two licenses in 1999, so we could upgrade them for $1906 (that is for both).  New mobile licenses are $1799 for locked and $2540 for concurrent.  We will most likely get academic pricing which takes of %40 so that would end up as $1079 each for locked and $1524 floating.  Maintence for new would also tack on $300 for each license. SysML and DODAF plugins cost extra and would be about $549 for both (each license).|
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[SmartDraw|http://www.smartdraw.com/exp/srd]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]|(/)|(/)|(x)|2.1|Yes, with MDG|(/)|C++, Java, C#, VB.Net, Visual Basic, Delphi, PHP, Python and ActionScript|Visual Studio and Eclipse|Yes, but I don't think automatically|Y|(?)|There are two pieces, Enterprise Architect(EA) and MDG Technology for SysML.  EA covers UML and MDG adds in SysML support. This one along with Borland one the Jolt award for 2006 for productivity. The EA tools did not really handle code well. Associations with multiplicity did not generate code correctly.|EA=$239,MDG=$100|
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue! Yep, I confirmed it.  You can tell the code generator what kind of collection you wish to use in the UML tool, but in SDE you cannot specify, it always uses object arrays (ouch!). So much for VP.|$1750 (no maint.)|
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* SmartSVN-4.0.3.zip
* SmartSVN-3.0.9.zip
* SmartSVN-3.0.7.zip
* SmartSVN-3.0.4.zip

\\
&nbsp;

----
h3. Macintosh

{color:#000000}({color}{color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color}{color:#000000}){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})

SmartSVN-4.0.3.zip

SmartSVN-3.0.9.zip

SmartSVN-3.0.7.zip

SmartSVN-3.0.4.zip

\\
\\
&nbsp;

----
h3. Macintosh

{color:#000000}({color}{color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color}{color:#000000}){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.3.zip|^smartsvn-win32-setup-nojre-4_0_3.zip]
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]
* SmartSVN-3.0.7.zip
* SmartSVN-3.0.4.zip
\\

----
h3. Macintosh

{color:#000000}({color}{color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color}{color:#000000}){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Altova UModel|http://www.altova.com/products/umodel/uml_tool.html]|(/)|(x)|(x)|2.2|(x)|(/)|Java,C#,VB.Net|None|(/)|(/)|Windows|The windows only thing is a big issue.|$189|
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test (see [Artisan Studio]).|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]|(/)|(/)|(/)|2.0|(x)|(/)|Java,C++|Eclipse|(/) The best by far|(/) Java,C++|(?)|After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | |Still have not gotten license issues cleared up so have not been able to test|$5500/$9625 float|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]|(/)|(/)|(/)|2.1|(/)|(/)|Java/J2EE, C#, C++, CORBA IDL, .NET, XML Schema, WSDL, Database Schema, DDL Generation|(?)|Yes for Java and C++|Yes, same list as Languages|(?)|I got it up and running.  It does not generate all the clean of HTML and I could not get the roundtrip engineering to work very well.  The option to refresh the code set was greyed out so I could not synch up the code.  After laboring through it, I think I had it setup to do the code round-trip, but when I ran it, most of the classes in my diagrams disappeared and all the buttons and windows in the different panes disappeared (this could just be a Mac thing, but ouch!).  I also could not find an easy way to define associations and have them link to getter methods in the code.|This is a bit involved.  I figured we would want Enterprise mobile licenses as this allows on user to have it on three machines.  Todd Anderson bought two licenses in 1999, so we could upgrade them for $1906 (that is for both).  New mobile licenses are $1799 for locked and $2540 for concurrent.  We will most likely get academic pricing which takes of %40 so that would end up as $1079 each for locked and $1524 floating.  Maintence for new would also tack on $300 for each license. SysML and DODAF plugins cost extra and would be about $549 for both (each license).|
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[SmartDraw|http://www.smartdraw.com/exp/srd]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]|(/)|(/)|(x)|2.1|Yes, with MDG|(/)|C++, Java, C#, VB.Net, Visual Basic, Delphi, PHP, Python and ActionScript|Visual Studio and Eclipse|Yes, but I don't think automatically|Y|(?)|There are two pieces, Enterprise Architect(EA) and MDG Technology for SysML.  EA covers UML and MDG adds in SysML support. This one along with Borland one the Jolt award for 2006 for productivity. The EA tools did not really handle code well. Associations with multiplicity did not generate code correctly.|EA=$239,MDG=$100|
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue! Yep, I confirmed it.  You can tell the code generator what kind of collection you wish to use in the UML tool, but in SDE you cannot specify, it always uses object arrays (ouch!). So much for VP.|$1750 (no maint.)|
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.3.zip|^smartsvn-win32-setup-nojre-4_0_3.zip]
* SmartSVN-3.0.9.zip
* SmartSVN-3.0.7.zip
* SmartSVN-3.0.4.zip
\\

----
h3. Macintosh

{color:#000000}({color}{color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color}{color:#000000}){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
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h3. *SmartSVN GUI Installation Files*


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h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* SmartSVN-4.0.3.zip
* SmartSVN-3.0.9.zip
* SmartSVN-3.0.7.zip
* SmartSVN-3.0.4.zip
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h3. Macintosh

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* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
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h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
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h3. *SmartSVN GUI Installation Files*


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h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.3.zip|^smartsvn-win32-setup-nojre-4_0_3.zip]
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]
* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|^SmartSVN.zip]
\\
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h3. Macintosh

{color:#000000}({color}{color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color}{color:#000000}){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
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h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
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h3. *SmartSVN GUI Installation Files*


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h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.3.zip|^smartsvn-win32-setup-nojre-4_0_3.zip]
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]
* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|^SmartSVN.zip]
\\ \\

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h3. Macintosh

{color:#000000}({color}{color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color}{color:#000000}){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

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h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
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h3. *SmartSVN GUI Installation Files*


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h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.3.zip|^smartsvn-win32-setup-nojre-4_0_3.zip]
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]
* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|^SmartSVN.zip]
\\

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h3. Macintosh

{color:#000000}({color}{color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color}{color:#000000}){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
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h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
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h3. *SmartSVN GUI Installation Files*


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h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.3.zip|^smartsvn-win32-setup-nojre-4_0_3.zip]
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]
* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip]
* SmartSVN-3.0.4.zip
\\

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h3. Macintosh

{color:#000000}({color}{color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color}{color:#000000}){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
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h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
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h3. *SmartSVN GUI Installation Files*


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h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.3.zip|^smartsvn-win32-setup-nojre-3_0_9.zip] {color:#ff0000}*\- NEW\!*{color}
* {color:#ff0000}[{color:#ff0000}SmartSVN-3.0.9.zip{color}|^smartsvn-win32-setup-nojre-3_0_9.zip]{color}
* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]\\
\\

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h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip] {color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]\\
\\

----
h3. Macintosh

* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]&nbsp; ({color:#ff0000}Mac&nbsp;OS X, version 10.4 or higher{color})
\\
\\
\\

----
h3. Linux

* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp; ({color:#ff0000}Note: Requires JRE 1.4.1 or higher{color})
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.3.zip|^smartsvn-win32-setup-nojre-3_0_9.zip] {color:#ff0000}*\- NEW\!*{color}
* {color:#000000}SmartSVN-3.0.9.zip{color}
* SmartSVN-3.0.7.zip
* SmartSVN-3.0.4.zip
\\

----
h3. Macintosh

({color:#ff0000}Note: all require{color} {color:#ff0000}Mac&nbsp;OS X, version 10.4 or higher){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.3.zip|^smartsvn-win32-setup-nojre-3_0_9.zip] {color:#ff0000}*\- NEW\!*{color}
* {color:#000000}SmartSVN-3.0.9.zip{color}
* SmartSVN-3.0.7.zip
* SmartSVN-3.0.4.zip
h3. \\
\---\-
Macintosh

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})

* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.3.zip|^smartsvn-win32-setup-nojre-3_0_9.zip] {color:#ff0000}*\- NEW\!*{color}
* {color:#000000}SmartSVN-3.0.9.zip{color}
* SmartSVN-3.0.7.zip
* SmartSVN-3.0.4.zip \\

----
h3. Macintosh

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.3.zip|^smartsvn-win32-setup-nojre-4_0_3.zip] {color:#ff0000}*\- NEW\!*{color}
* {color:#000000}[{color:#000000}SmartSVN-3.0.9.zip{color}|^smartsvn-win32-setup-nojre-3_0_9.zip]{color}
* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|^SmartSVN.zip]
\\

----
h3. Macintosh

({color:#ff0000}Note: all require{color} {color:#ff0000}Mac&nbsp;OS X, version 10.4 or higher){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.3.zip|^smartsvn-win32-setup-nojre-4_0_3.zip] {color:#ff0000}*\- NEW\!*{color}
* {color:#000000}SmartSVN-3.0.9.zip{color}
* SmartSVN-3.0.7.zip
* SmartSVN-3.0.4.zip
\\

----
h3. Macintosh

({color:#ff0000}Note: all require{color} {color:#ff0000}Mac&nbsp;OS X, version 10.4 or higher){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test (see [Artisan Studio]).|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]|(/)|(/)|(/)|2.0|(x)|(/)|Java,C++|Eclipse|(/) The best by far|(/) Java,C++|(?)|After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | |Still have not gotten license issues cleared up so have not been able to test|$5500/$9625 float|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]|(/)|(/)|(/)|2.1|(/)|(/)|Java/J2EE, C#, C++, CORBA IDL, .NET, XML Schema, WSDL, Database Schema, DDL Generation|(?)|Yes for Java and C++|Yes, same list as Languages|(?)|I got it up and running.  It does not generate all the clean of HTML and I could not get the roundtrip engineering to work very well.  The option to refresh the code set was greyed out so I could not synch up the code.  After laboring through it, I think I had it setup to do the code round-trip, but when I ran it, most of the classes in my diagrams disappeared and all the buttons and windows in the different panes disappeared (this could just be a Mac thing, but ouch!).  I also could not find an easy way to define associations and have them link to getter methods in the code.|This is a bit involved.  I figured we would want Enterprise mobile licenses as this allows on user to have it on three machines.  Todd Anderson bought two licenses in 1999, so we could upgrade them for $1906 (that is for both).  New mobile licenses are $1799 for locked and $2540 for concurrent.  We will most likely get academic pricing which takes of %40 so that would end up as $1079 each for locked and $1524 floating.  Maintence for new would also tack on $300 for each license. SysML and DODAF plugins cost extra and would be about $549 for both (each license).|
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[SmartDraw|http://www.smartdraw.com/exp/srd]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]|(/)|(/)|(x)|2.1|Yes, with MDG|(/)|C++, Java, C#, VB.Net, Visual Basic, Delphi, PHP, Python and ActionScript|Visual Studio and Eclipse|Yes, but I don't think automatically|Y|(?)|There are two pieces, Enterprise Architect(EA) and MDG Technology for SysML.  EA covers UML and MDG adds in SysML support. This one along with Borland one the Jolt award for 2006 for productivity. The EA tools did not really handle code well. Associations with multiplicity did not generate code correctly.|EA=$239,MDG=$100|
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue! Yep, I confirmed it.  You can tell the code generator what kind of collection you wish to use in the UML tool, but in SDE you cannot specify, it always uses object arrays (ouch!). So much for VP.|$1750 (no maint.)|
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.3.zip|^smartsvn-win32-setup-nojre-4_0_3.zip] {color:#ff0000}*\- NEW\!*{color}
* {color:#000000}\[{color}{color:#000000}SmartSVN-3.0.9.zip{color}\|^smartsvn-win32-setup-nojre-3_0_9.zip\]
\* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip]
\* [SmartSVN-3.0.4.zip|^SmartSVN.zip]

\\
\\
&nbsp;

----
h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color}{color:#000000}){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* {color:#000000}SmartSVN-4.0.3.zip{color}
* {color:#000000}SmartSVN-3.0.9.zip{color}
* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|^SmartSVN.zip]

\\
\\
&nbsp;

----
h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color}{color:#000000}){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.3.zip|^smartsvn-win32-setup-nojre-4_0_3.zip] {color:#ff0000}*\- NEW\!*{color}
* {color:#000000}\[{color}{color:#000000}SmartSVN-3.0.9.zip{color}\|^smartsvn-win32-setup-nojre-3_0_9.zip\]
\* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip]
\* [SmartSVN-3.0.4.zip|^SmartSVN.zip]
\\
\---\-
h3. Macintosh

(Note: all require {color:#ff0000}Mac&nbsp;OS X, version 10.4 or higher){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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There are&nbsp;two recommended CVS Clients to access the MBARI CVS Respository including:&nbsp;{color:#ff0000}{*}WinCVS{*}{color} and {color:#ff0000}{*}SmartCVS{*}{color}.&nbsp;&nbsp; Both clients work for all major operating systems including Windows, Macintosh, and Linux systems.&nbsp;The key bits of information to use when setting up either client are the following:
* {color:#0000cc}Your access method needs to be set to&nbsp;{color}{color:#0000cc}{*}pserver{*}{color}{color:#0000cc}&nbsp;(SmartCVS) or{color} {color:#0000cc}{*}passwd file on server{*}{color} {color:#0000cc}(WinCVS){color}
* {color:#0000cc}User&nbsp; (Your MBARI user/e-mail&nbsp;account, e.g.,{color} {color:#0000cc}{_}salamy{_}{color}{color:#0000cc}){color}
* {color:#0000cc}Repository Server (MBARI CVS Repository is hosted on{color} {color:#0000cc}{*}{_}moonjelly.shore.mbari.org{_}{*}{color}{color:#0000cc}){color}
* {color:#0000cc}CVSROOT ({color}{color:#0000cc}{*}_/home/cvs{_}{*}{color}{color:#0000cc}){color}

Thus, the full CVSROOT path for user _salamy_ would be:&nbsp;&nbsp;&nbsp; salamy@moonjelly.shore.mbari.org:/home/cvs&nbsp;

----
\\

h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Windows-7.1.1.zip|^smartcvs-win32-setup-nojre-7_1_1.zip|SmartCVS Windows version 7.1.1] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOSX-7.1.1.tar.gz|^smartcvs-generic-7_1_1.tar.gz|SmartCVS Macintosh Version 7.1.1] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartSVN-Linux-7.1.1.tar.gz|^smartcvs-generic-7_1_1.tar.gz|SmartSVN Linux Version 7.1.1] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}({color}{color:#0066cc}{*}NOTE:*{color}{color:#0066cc}&nbsp;Setup same for MacCVS and gCVS as well){color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS Getting-Started Tutorial|^smartcvs-tutorial.pdf] \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

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There are&nbsp;two recommended CVS Clients to access the MBARI CVS Respository including:&nbsp;{color:#ff0000}{*}WinCVS{*}{color} and {color:#ff0000}{*}SmartCVS{*}{color}.&nbsp;&nbsp; Both clients work for all major operating systems including Windows, Macintosh, and Linux systems.&nbsp;The key bits of information to use when setting up either client are the following:
* {color:#0000cc}Your access method needs to be set to&nbsp;{color}{color:#0000cc}{*}pserver{*}{color}{color:#0000cc}&nbsp;(SmartCVS) or{color} {color:#0000cc}{*}passwd file on server{*}{color} {color:#0000cc}(WinCVS){color}
* {color:#0000cc}User&nbsp; (Your MBARI user/e-mail&nbsp;account, e.g.,{color} {color:#0000cc}{_}salamy{_}{color}{color:#0000cc}){color}
* {color:#0000cc}Repository Server (MBARI CVS Repository is hosted on{color} {color:#0000cc}{*}{_}moonjelly.shore.mbari.org{_}{*}{color}{color:#0000cc}){color}
* {color:#0000cc}CVSROOT ({color}{color:#0000cc}{*}_/home/cvs{_}{*}{color}{color:#0000cc}){color}

Thus, the full CVSROOT path for user _salamy_ would be:&nbsp;&nbsp;&nbsp; salamy@moonjelly.shore.mbari.org:/home/cvs&nbsp;

----
\\

h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Windows-7.1.1.zip|^smartcvs-win32-setup-nojre-7_1_1.zip|SmartCVS Windows version 7.1.1] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOSX-7.1.3.tar.gz|^smartcvs-macosx-7_1_3.tar.gz|SmartCVS Macintosh Version 7.1.3] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartSVN-Linux-7.1.1.tar.gz|^smartcvs-generic-7_1_1.tar.gz|SmartSVN Linux Version 7.1.1] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}({color}{color:#0066cc}{*}NOTE:*{color}{color:#0066cc}&nbsp;Setup same for MacCVS and gCVS as well){color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS Getting-Started Tutorial|^smartcvs-tutorial.pdf] \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

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h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-6.5.5.zip|^smartsvn-windows-x86-setup-nojre-6_5_5.zip|SmartSVN for Windows version 6.5.5]&nbsp;&nbsp; {color:#ff0000}*\- NEW\!*{color}

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h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-Mac-6.5.5.tar.gz|^smartsvn-macosx-6_5_5.tar.gz|SmartSVN Macintosh version 6.5.5]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}

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----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-Linux-6.5.5.tar.gz|^smartsvn-generic-6_5_5.tar.gz|SmartSVN Linux version 6.5.5]&nbsp;{color:#ff0000}*\- NEW\!*{color}

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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by http://www.seadatanet.org/
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo (http://www.iwceexpo.com)
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: <!--  /* Font Definitions */ @font-face 	{font-family:Arial; 	panose-1:2 11 6 4 2 2 2 2 2 4; 	mso-font-charset:0; 	mso-generic-font-family:auto; 	mso-font-pitch:variable; 	mso-font-signature:3 0 0 0 1 0;}  /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal 	{mso-style-parent:""; 	margin:0in; 	margin-bottom:.0001pt; 	mso-pagination:widow-orphan; 	font-size:12.0pt; 	font-family:"Times New Roman"; 	mso-fareast-font-family:"Times New Roman"; 	mso-bidi-font-family:"Times New Roman";} @page Section1 	{size:8.5in 11.0in; 	margin:1.0in 1.25in 1.0in 1.25in; 	mso-header-margin:.5in; 	mso-footer-margin:.5in; 	mso-paper-source:0;} div.Section1 	{page:Section1;} -->{color:black}Coral Reef Environmental Observatory Network&nbsp; http://www.coralreefeon.org/ &nbsp;{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See http://code.google.com/p/nctoolbox/)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[----
*Welcome to CVS\!*&nbsp; CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp; You have requested to be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).

\\
&nbsp;
{noformat}
PERMISSIONS
Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.  If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. moonjelly is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.   If you cannot for any reason, please let me know.
{noformat}
{noformat}
PASSWORD ACCESS REQUIRED
Access to the repository requires another (separate) password.  NOTE: To allow you access to the repository, I will need you to supply a CVS repository password.
To do this, access the MBARI network (usually through a command prompt, Cygwin window, or Linux terminal) , telnet and login to moonjelly with your MBARI password.  Next, type the  following at the prompt: encryptCVSpw
This runs a script that outputs an encrypted version of your password.
!!! Please e-mail me the encrypted text (exactly as shown) so that I may add you to the repository password list. I will send you an e-mail when you are able to access the repository. !!!


{noformat}
{noformat}
CVS GUIs
GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.  I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2" link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.
The gcvs rpm can be downloaded for most RedHat systems from here:
http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html
For the most in-depth cvs information, please see the CVS manual at: http://www.cvshome.org/docs/manual/.
You can also simply "view" the current repository tree structure at: http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/ . 
This will allow you to simply read any of the project modules.  Let me know how it works and if you have any problems. In addition,
Please remember to e-mail your encrypted password as soon as possible to me at: salamy@mbari.org.

{noformat}
*Regards, -* *Karen A. Salamy* *(*{*}{_}MBARI CVS administrator)_* *\- salamy@mbari.org*
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit their respective websites.

Contact Kevin Gomes [mailto:kgomes@mbari.org], Brian Schlining [mailto:brian@mbari.org] or Kent Headley [mailto:headley@mbari.org] with questions or permission requests for certain tools.

{tip:title=External Availability}
Please note that Confluence, JIRA, and Alfresco are all available outside the MBARI firewall and can have external collaborator accounts that are not MBARI accounts.  This was a desirable feature of these tools and allows us to externally collaborate without risking security breaches at MBARI.
{tip}

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.
----
h3. Content Management with [Alfresco|https://alfresco.mbari.org/alfresco]

Alfresco is a Content Management System (CMS) intended to replace the Project Library on Tornado as the repository for MBARI project documentation. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

{info:title=Accounting Creates Projects in Alfresco}
One of the main benefits of Alfresco is that it can interact with our accounting system in an automated fashion. Because of this, we have the accounting system currently creating project spaces and directory structures in Alfresco automatically.  This allows the accounting software to then export all accounting activity (PDFs of AMEX, PO's, etc.) to the Alfresco spaces automatically.
{info}

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password without using "shore\" in front) to see the project library materials. The *Projects* folder is the space that contains the content for projects at MBARI.

To create a short cut to the Projects folder (or any folder), enter that folder, then select "More Actions/View Details", then "Create Shortcut" (on the right side of the page).  This will create a shortcut that will be available in the "Shelf".  To view the shortcuts in your "Shelf", click on the down arrow next to "Navigtor" on the left hand sidebar menu, then select "Shelf" and you will see your created shortcuts.

Here are some useful links related to MBARI's installation of Alfresco:
* [Alfresco's Homepage|http://www.alfresco.com/]
* [Alfresco's Developer Home Page|http://wiki.alfresco.com/wiki/Main_Page]
* [Alfresco's Enterprise Customer Portal|https://network.alfresco.com/extranet/]
* [Deployment Information at MBARI]
* [Installation Notes]
* [alfresco.mbari.org Installation Notes]
* [alfresco-test.shore.mbari.org Installation Notes]

----
h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts an externally accessable Maven repository at [https://oceana.mbari.org/maven2], an internal repository at [http://seaspray.shore.mbari.org:8082/archiva/repository/internal/] and a repository manager at [http://seaspray.shore.mbari.org:8082/archiva]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modeling with UML (JBuilder 2008 Enterprise)

You can download JBuilder 2008 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded and installed, you need to copy the following [.slip|https://alfresco.mbari.org/alfresco/webdav/Engineering/Tools/Collaboration%20Tools/CodeGear%20JBuilder/concurrent_31474.slip] file to the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://confluence.mbari.org].

Contact Kevin Gomes [mailto:kgomes@mbari.org], Brian Schlining [mailto:brian@mbari.org] or Kent Headley [mailto:headley@mbari.org] with questions or permission requests for certain tools.

{tip:title=External Availability}
Please note that Confluence, JIRA, and Alfresco are all available outside the MBARI firewall and can have external collaborator accounts that are not MBARI accounts.  This was a desirable feature of these tools and allows us to externally collaborate without risking security breaches at MBARI.
{tip}

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.
----
h3. Content Management with [Alfresco|https://alfresco.mbari.org/alfresco]

Alfresco is a Content Management System (CMS) intended to replace the Project Library on Tornado as the repository for MBARI project documentation. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

{info:title=Accounting Creates Projects in Alfresco}
One of the main benefits of Alfresco is that it can interact with our accounting system in an automated fashion. Because of this, we have the accounting system currently creating project spaces and directory structures in Alfresco automatically.  This allows the accounting software to then export all accounting activity (PDFs of AMEX, PO's, etc.) to the Alfresco spaces automatically.
{info}

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password without using "shore\" in front) to see the project library materials. The *Projects* folder is the space that contains the content for projects at MBARI.

To create a short cut to the Projects folder (or any folder), enter that folder, then select "More Actions/View Details", then "Create Shortcut" (on the right side of the page).  This will create a shortcut that will be available in the "Shelf".  To view the shortcuts in your "Shelf", click on the down arrow next to "Navigtor" on the left hand sidebar menu, then select "Shelf" and you will see your created shortcuts.

Here are some useful links related to MBARI's installation of Alfresco:
* [Deployment Information]
* [Installation Notes]
* [alfresco.mbari.org Installation Notes]
* [alfresco-test.shore.mbari.org Installation Notes]

----
h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts an externally accessable Maven repository at [https://oceana.mbari.org/maven2], an internal repository at [http://seaspray.shore.mbari.org:8082/archiva/repository/internal/] and a repository manager at [http://seaspray.shore.mbari.org:8082/archiva]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modeling with UML (JBuilder 2008 Enterprise)

You can download JBuilder 2008 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded and installed, you need to copy the following [.slip|https://alfresco.mbari.org/alfresco/webdav/Engineering/Tools/Collaboration%20Tools/CodeGear%20JBuilder/concurrent_31474.slip] file to the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[----
*Welcome to CVS\!*&nbsp; CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp; You have requested to be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).\\

*PERMISSIONS*
Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. _moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot for any reason, please let me know.\\

*PASSWORD ACCESS REQUIRED*
Access to the repository requires another (separate) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a&nbsp;CVS repository password.*{color}

To do this, access the MBARI network (_usually through a command prompt, Cygwin window, or Linux terminal_)&nbsp;, telnet and login to moonjelly with your MBARI password.&nbsp;&nbsp;Next, type the&nbsp; following at the prompt: {color:red}{*}encryptCVSpw{*}{color}

This runs a script that outputs an encrypted version of your password.

{color:#ff0000}{*}+\!\!\! Please e-mail me the encrypted text (exactly as shown) so{+}{*}{color} {color:#ff0000}{*}{+}that I may add you to the repository password list. I will{+}{*}{color} {color:#ff0000}{*}{+}send you an e-mail when you are able to access the repository. \!\!\!+{*}{color}\\

*CVS GUIs*
GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2"&nbsp;link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here:
[http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .&nbsp;
{color:black}This will allow you to simply read any of the project modules.&nbsp;{color} Let me know how it works and if you have any problems. In addition,

Please&nbsp;remember to&nbsp;e-mail your encrypted password as soon as possible to me at: salamy@mbari.org.
\\ \\

Regards, - *Karen A. Salamy* (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit their respective websites.

Contact Kevin Gomes [mailto:kgomes@mbari.org], Brian Schlining [mailto:brian@mbari.org] or Kent Headley [mailto:headley@mbari.org] with questions or permission requests for certain tools.

{tip:title=External Availability}
Please note that Confluence, JIRA, and Alfresco are all available outside the MBARI firewall and can have external collaborator accounts that are not MBARI accounts.  This was a desirable feature of these tools and allows us to externally collaborate without risking security breaches at MBARI.
{tip}

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.
----
h3. Content Management with [Alfresco|https://alfresco.mbari.org/alfresco]

Alfresco is a Content Management System (CMS) intended to replace the Project Library on Tornado as the repository for MBARI project documentation. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

{info:title=Accounting Creates Projects in Alfresco}
One of the main benefits of Alfresco is that it can interact with our accounting system in an automated fashion. Because of this, we have the accounting system currently creating project spaces and directory structures in Alfresco automatically.  This allows the accounting software to then export all accounting activity (PDFs of AMEX, PO's, etc.) to the Alfresco spaces automatically.
{info}

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password without using "shore\" in front) to see the project library materials. The *Projects* folder is the space that contains the content for projects at MBARI.

To create a short cut to the Projects folder (or any folder), enter that folder, then select "More Actions/View Details", then "Create Shortcut" (on the right side of the page).  This will create a shortcut that will be available in the "Shelf".  To view the shortcuts in your "Shelf", click on the down arrow next to "Navigtor" on the left hand sidebar menu, then select "Shelf" and you will see your created shortcuts.

Here are some useful links related to MBARI's installation of Alfresco:
* [Alfresco's Homepage|http://www.alfresco.com/]
* [Alfresco's Developer Home Page|http://wiki.alfresco.com/wiki/Main_Page]
* [Alfresco's Enterprise Customer Portal|https://network.alfresco.com/extranet/]
* [Deployment Information for MBARI's Alfresco Installation|Deployment Information]
* [Installation Notes]
* [alfresco.mbari.org Installation Notes]
* [alfresco-test.shore.mbari.org Installation Notes]

----
h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts an externally accessable Maven repository at [https://oceana.mbari.org/maven2], an internal repository at [http://seaspray.shore.mbari.org:8082/archiva/repository/internal/] and a repository manager at [http://seaspray.shore.mbari.org:8082/archiva]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modeling with UML (JBuilder 2008 Enterprise)

You can download JBuilder 2008 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded and installed, you need to copy the following [.slip|https://alfresco.mbari.org/alfresco/webdav/Engineering/Tools/Collaboration%20Tools/CodeGear%20JBuilder/concurrent_31474.slip] file to the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. http://en.wikipedia.org/wiki/Grid_computing
# GUI: Graphical User Interface
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[----
*Welcome to CVS\!*&nbsp; CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp; You have requested to be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

\\

*PERMISSIONS*
Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. moonjelly is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot for any reason, please let me know.

\\
&nbsp;

*PASSWORD ACCESS*
Access to the repository requires another (separate) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network, telnet and login to moonjelly and type the&nbsp; following at the prompt: {color:red}{*}encryptCVSpw{*}{color}
This runs a script that outputs an encrypted version of your password.

*+\!\!\! Please e-mail me the encrypted text (exactly as shown) so{+}* *{+}that I may add you to the repository password list. I will{+}* *{+}send you an e-mail when you are able to access the repository. \!\!\!+*
\\

\\
&nbsp;*CVS GUIs*
GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2"&nbsp;link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs. The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html] For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/]. You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. In addition, PLEASE remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

*Regards, -* *Karen A. Salamy* *(*{*}{_}MBARI CVS administrator)_* *\- salamy@mbari.org*
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. http://en.wikipedia.org/wiki/Grid_computing
# GUI: Graphical User Interface
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GUI: Graphical User Interface
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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*Welcome to CVS\!*&nbsp; CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp; You have requested to be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).\\

\\

*PERMISSIONS*
Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. moonjelly is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot for any reason, please let me know. \\


PASSWORD ACCESS
Access to the repository requires another (separate) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network, telnet and login to moonjelly and type the&nbsp; following at the prompt: {color:red}{*}encryptCVSpw{*}{color}
This runs a script that outputs an encrypted version of your password.


*+\!\!\! Please e-mail me the encrypted text (exactly as shown) so{+}* *{+}that I may add you to the repository password list. I will{+}* *{+}send you an e-mail when you are able to access the repository. \!\!\!+* \\  *CVS GUIs*
GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2"&nbsp;link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs. The gcvs rpm can be downloaded for most RedHat systems from here: http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html For the most in-depth cvs information, please see the CVS manual at: http://www.cvshome.org/docs/manual/. You can also simply "view" the current repository tree structure at: http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/ .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. In addition, PLEASE remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;
{noformat}
&nbsp;
{noformat}
*Regards, -* *Karen A. Salamy* *(*{*}{_}MBARI CVS administrator)_* *\- salamy@mbari.org*
\\]]></property>
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<property name="body"><![CDATA[----
*Welcome to CVS\!*&nbsp; CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp; You have requested to be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

\\

*PERMISSIONS*
Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. moonjelly is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot for any reason, please let me know.

\\
&nbsp;

*PASSWORD ACCESS*
Access to the repository requires another (separate) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network, telnet and login to moonjelly and type the&nbsp; following at the prompt: {color:red}{*}encryptCVSpw{*}{color}
This runs a script that outputs an encrypted version of your password.

*+\!\!\! Please e-mail me the encrypted text (exactly as shown) so{+}* *{+}that I may add you to the repository password list. I will{+}* *{+}send you an e-mail when you are able to access the repository. \!\!\!+* \\

\\
&nbsp;*CVS GUIs*
GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2"&nbsp;link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs. The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html] For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/]. You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. In addition, PLEASE remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;
{noformat}
&nbsp;
{noformat}
*Regards, -* *Karen A. Salamy* *(*{*}{_}MBARI CVS administrator)_* *\- salamy@mbari.org*
\\]]></property>
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h3. *Welcome to CVS\!*

CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp;&nbsp;Someone has&nbsp;requested that you be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

h3. \\


h3. *PERMISSIONS*

Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. moonjelly is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot for any reason, please let me know.

\\
&nbsp;

h3. *PASSWORD ACCESS*

Access to the repository requires another (separate) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network, telnet and login to moonjelly and type the&nbsp; following at the prompt: {color:red}{*}encryptCVSpw{*}{color}
This runs a script that outputs an encrypted version of your password.

*+\!\!\! Please e-mail me the encrypted text (exactly as shown) so{+}* *{+}that I may add you to the repository password list. I will{+}* *{+}send you an e-mail when you are able to access the repository. \!\!\!+*

\\
&nbsp;

h3. *CVS GUIs*

GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2"&nbsp;link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs. The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html] For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/]. You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. In addition, PLEASE remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

Regards, - Karen A. Salamy (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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<property name="body"><![CDATA[----
*Welcome to CVS\!*&nbsp; CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp; You have requested to be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

\\

*PERMISSIONS*
Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. moonjelly is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot for any reason, please let me know.

\\
&nbsp;

*PASSWORD ACCESS*
Access to the repository requires another (separate) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network, telnet and login to moonjelly and type the&nbsp; following at the prompt: {color:red}{*}encryptCVSpw{*}{color}
This runs a script that outputs an encrypted version of your password.

*+\!\!\! Please e-mail me the encrypted text (exactly as shown) so{+}* *{+}that I may add you to the repository password list. I will{+}* *{+}send you an e-mail when you are able to access the repository. \!\!\!+*

\\
&nbsp;

\\
&nbsp;*CVS GUIs*
GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2"&nbsp;link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs. The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html] For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/]. You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. In addition, PLEASE remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

*Regards, -* *Karen A. Salamy* *(*{*}{_}MBARI CVS administrator)_* *\- salamy@mbari.org*
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<property name="body"><![CDATA[----
h3. *Welcome to CVS\!*

CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp; You have requested to be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

h3. \\


h3. *PERMISSIONS*

Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. moonjelly is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot for any reason, please let me know.

\\
&nbsp;

h3. *PASSWORD ACCESS*

Access to the repository requires another (separate) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network, telnet and login to moonjelly and type the&nbsp; following at the prompt: {color:red}{*}encryptCVSpw{*}{color}
This runs a script that outputs an encrypted version of your password.

*+\!\!\! Please e-mail me the encrypted text (exactly as shown) so{+}* *{+}that I may add you to the repository password list. I will{+}* *{+}send you an e-mail when you are able to access the repository. \!\!\!+*

\\
&nbsp;

h3. *CVS GUIs*

GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2"&nbsp;link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs. The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html] For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/]. You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. In addition, PLEASE remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

Regards, - Karen A. Salamy (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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<property name="body"><![CDATA[h3.
\\

h2. Welcome to CVS\!


----
h2. Setting up the CVS GUI on your computer


h3.


----
&nbsp;&nbsp;

h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms.  http://www.act-us.info/
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. http://www.alfresco.com http://alfresco.mbari.org
# ALOHA-MARS: http://alohamooring.apl.washington.edu/ ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of ~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). http://seahurst.apl.washington.edu/mars.php
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection http://www.mbari.org/aved/
# AWW: All was well. http://www.jkrowling.com/en/
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System http://www.mbari.org/expeditions/Pulse53/gear.htm
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology http://en.wikipedia.org/wiki/Caltech  
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure http://en.wikipedia.org/wiki/Cyberinfrastructure
# CeNCOOS: Central and Northern California Ocean Observing System http://www.cencoos.org/ 
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine http://www.webopedia.com/TERM/C/CNAME.htm 
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison http://www.cs.wisc.edu/condor/
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. http://www.unixgeeks.org/security/newbie/unix/cron-1.html 
# CTD: Conductivity, Temperature, and Depth http://www.whoi.edu/instruments/viewInstrument.do?id=1003
# CVS: Concurrent Versions System; maintains control of history of code/documents 
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. http://en.wikipedia.org/wiki/Demilitarized_zone_(computing) 
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering 
# eGY: the Electronic Geophysical Year http://www.egy.org/
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring.  http://www.mbari.org/mars/general/eits.html
# EOM: Electro-Optical-Mechanical
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network http://www.oceanlab.abdn.ac.uk/research/esonet.php
# ESP: Environmental Sample Processor - Chris Scholin et al. http://www.mbari.org/muse/platforms/ESP.htm
## Darlene was the 1st generation ESP 
## GiGi The first 'second generation' ESP instrument 
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument 
## Bruce Another 'third generation' ESP instrument 
## MOE A third gen. instrument with the MFB connected 
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer 
# GEOSS: Global Earth Observation System of Systems http://www.epa.gov/geoss/
# GUI: Graphical User Interface 
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program 
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces 
# IDE: Integrated Development Environment      
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C++ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See http://www.iode.org/index.php?option=com_content&task=view&id=74 for details.
# IO: Implementing Organization http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf
# IOC: Intergovernmental Oceanographic Commission, http://ioc.unesco.org/iocweb/index.php
# IODE: International Oceanographic Data Exchange, http://www.iode.org
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, http://ioc.unesco.org/iocweb/index.php
# JIRA: A bug tracking, issue tracking, and project management application http://www.atlassian.com/software/jira/
# JOI: Joint Oceanographic Institutions http://www.joiscience.org/joi
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode 
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap 
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool.  http://maven.apache.org/
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). (http://marinemetadata.org/meta-t )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP 
# MMI: Marine Metadata Initiative http://marinemetadata.org/
# MOBB: Monterey Ocean Bottom Broadband project 
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] http://en.wikipedia.org/wiki/Modbus
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. http://mule.codehaus.org/display/MULE/Home
# MV: Medium Voltage (converter); located in node power supply of MARS 
# Nagios: software to monitor all types of computer and network services. http://www.nagios.org/
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form)             http://www.unidata.ucar.edu/software/netcdf/conventions.html
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. http://www.opengeospatial.org/
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. http://www.ogf.org/
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. http://www.oostethys.org/
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) http://www.pc104.org
# PCA: Principal component analysis. http://en.wikipedia.org/wiki/Principal_components_analysis
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?") 
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. http://en.wikipedia.org/wiki/PH
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor". 
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives http://en.wikipedia.org/wiki/RAID
# RBI: Runs Batted In
# RC: Radio controlled (airplane) 
# RCO: Regional Cabled Observatory http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems http://www.rosys.com/
# ROV: Remotely Operated Vehicle 
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. http://en.wikipedia.org/wiki/RS-232
# RSN: Regional Scale Node. See RCO. http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. (http://www.seadatanet.org/)
# SensorML: not an acronym; markup language to describe sensors and their data. http://vast.uah.edu/SensorML/  
# SIFT: Scale-invariant feature transform http://en.wikipedia.org/wiki/Scale-invariant_feature_transform
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module 
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/]  [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) http://www.tsa.gov/what_we_do/layers/twic/index.shtm
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. http://en.wikipedia.org/wiki/UART
# UCB: University of California-Berkeley 
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply 
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. http://www.venus.uvic.ca/
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language 
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, http://www.wmo.ch
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language http://en.wikipedia.org/wiki/XML
# XSD -- XML Schema Definition http://en.wikipedia.org/wiki/XML_Schema
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<property name="body"><![CDATA[----
h3. *Welcome to CVS\!*

CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp;&nbsp;Someone has&nbsp;requested that you be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly ([salamy@mbari.org]).
\\

h3. \\


h3. *PERMISSIONS*

Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. moonjelly is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot for any reason, please let me know.

\\
&nbsp;

h3. *PASSWORD ACCESS*

Access to the repository requires another (separate) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network, telnet and login to moonjelly and type the&nbsp; following at the prompt: {color:red}{*}encryptCVSpw{*}{color}
This runs a script that outputs an encrypted version of your password.

*+\!\!\! Please e-mail me the encrypted text (exactly as shown) so{+}* *{+}that I may add you to the repository password list. I will{+}* *{+}send you an e-mail when you are able to access the repository. \!\!\!+*

\\
&nbsp;

h3. *CVS GUIs*

GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2"&nbsp;link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs. The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html] For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/]. You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. In addition, PLEASE remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

Regards, - Karen A. Salamy (_MBARI CVS administrator)_ \- salamy@mbari.org
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<property name="body"><![CDATA[h3.


h2. Welcome to CVS\!


----
h2. Setting up the CVS GUI on your computer


h3.

----

&nbsp;&nbsp;

h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
&nbsp;]]></property>
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<property name="body"><![CDATA[h3.


h3. Welcome to CVS\!


----
h3. Setting up the CVS GUI on your computer


h3.


h2.

----
&nbsp;&nbsp;


h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
&nbsp;]]></property>
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<property name="body"><![CDATA[*Welcome to CVS\!*&nbsp; CVS is the MBARI Software Engineering source code repository which resides on the Linux server 'moonjelly'.&nbsp; You have requested to be added to the module called "ESP" in the CVS repository.&nbsp; You have been given access to the *"ESP"*, and "*cvs*" modules (projects).&nbsp; As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} is one of these two. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly.

*PERMISSIONS*
Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. moonjelly is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot for any reason, please let me know.
&nbsp;

*PASSWORD ACCESS REQUIRED*
Access to the repository requires another (separate) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network, telnet and login to moonjelly and type the&nbsp; following at the prompt: {color:red}{*}encryptCVSpw{*}{color}

This runs a script that outputs an encrypted version of your password.

*+\!\!\! Please e-mail me the encrypted text (exactly as shown) so{+}* *{+}that I may add you to the repository password list. I will{+}* *{+}send you an e-mail when you are able to access the repository. \!\!\!+* \\

*CVS GUIs*
GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2"&nbsp;link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here:
[http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .&nbsp;
{color:black}This will allow you to simply read any of the project modules.&nbsp;{color} Let me know how it works and if you have any problems. In addition,

*PLEASE* remember to send me your encrypted password as soon as possible.
&nbsp;
Regards, - *Karen A. Salamy* (_MBARI CVS administrator)_ \- salamy@mbari.org\\]]></property>
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<property name="body"><![CDATA[h3.


h2. Welcome to CVS\!

Welcome to CVS\!&nbsp; CVS is the MBARI Software Engineering source code repository which resides on the Linux server 'moonjelly'.
You have requested to be added to the module called "ESP" in the CVS repository.&nbsp; You have been given access to the *"ESP"*,
and "*cvs*" modules (projects).&nbsp; As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color}
or {color:blue}{*}group{*}{color} is one of these two. If you need to be added to another module in the future, please let me know as I am the CVS system
administrator for moonjelly. *PERMISSIONS*
Permissions for these modules are set-up so that all files in the module
are made writable only for members of the specified group.&nbsp; If someone
is not part of a particular group, they will not have access to write to any
files under that directory. These permissions are set recursively throughout
the project for security purposes. moonjelly is on the NIS server at MBARI
so you should be able to access the system through telnet via your main
MBARI password.&nbsp;&nbsp; If you cannot for any reason, please let me know.
&nbsp;&nbsp;
Access to the repository requires another (separate) password.
{color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color}
{color:red}{*}a cvs repository password.*{color} To do this, access the MBARI network, telnet
and login to moonjelly and type the&nbsp; following at the prompt: {color:red}{*}encryptCVSpw{*}{color}
This runs a script that outputs an encrypted version of your password.
*+\!\!\! Please e-mail me the encrypted text (exactly as shown) so{+}*
*{+}that I may add you to the repository password list. I will{+}*
*{+}send you an e-mail when you are able to access the repository. \!\!\!+* *CVS GUIs*
GUIs are the main way users interact with the repository to checkout, edit,
and checkin files. Several of these include WinCVS (windows-based), gcvs
(Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based
version). You may also use the command line if you do not wish to use a GUI.
I have written up a basic "getting started" document for repository users. At
the moment, however, it outlines installing and working with WinCVS only
since Windows is the main OS used at MBARI. I am not sure if you plan to
use a GUI or command line. If you wish to try out WinCVS, please review the
"Setting up WinCVS_1.2" document attached. You may also reference the guide should you wish to use the Linux
version of the GUI, gcvs, as the menu structure is very similar for both
GUIs. The gcvs rpm can be downloaded for most RedHat systems from here:
[http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html] For the most in-depth cvs information, please see the CVS manual at:
[http://www.cvshome.org/docs/manual/]. You can also simply "view" the current repository tree structure at:
[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .&nbsp;
{color:black}This will allow you to simply read any of the project modules.{color}
Let me know how it works and if you have any problems. In addition,
PLEASE remember to send me your encrypted password as soon
as possible.
&nbsp;
Regards, - Karen]]></property>
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<property name="body"><![CDATA[----
*Welcome to CVS\!*&nbsp; CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp; You have requested to be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\ \\

*PERMISSIONS*
Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. _moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot for any reason, please let me know.
\\ \\

*PASSWORD ACCESS REQUIRED*
Access to the repository requires another (separate) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a&nbsp;CVS repository password.*{color}

To do this, access the MBARI network (_usually through a command prompt, Cygwin window, or Linux terminal_)&nbsp;, telnet and login to moonjelly with your MBARI password.&nbsp;&nbsp;Next, type the&nbsp; following at the prompt: {color:red}{*}encryptCVSpw{*}{color}

This runs a script that outputs an encrypted version of your password.

{color:#ff0000}{*}+\!\!\! Please e-mail me the encrypted text (exactly as shown) so{+}{*}{color} {color:#ff0000}{*}{+}that I may add you to the repository password list. I will{+}{*}{color} {color:#ff0000}{*}{+}send you an e-mail when you are able to access the repository. \!\!\!+{*}{color}
\\ \\

*CVS GUIs*
GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2"&nbsp;link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here:
[http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .&nbsp;
{color:black}This will allow you to simply read any of the project modules.&nbsp;{color} Let me know how it works and if you have any problems. In addition,

Please&nbsp;remember to&nbsp;e-mail your encrypted password as soon as possible to me at: salamy@mbari.org.
\\ \\

Regards, - *Karen A. Salamy* (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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<property name="body"><![CDATA[----

*Welcome to CVS\!*&nbsp; CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp; You have requested to be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).\\

*PERMISSIONS*
Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. _moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot for any reason, please let me know.\\

*PASSWORD ACCESS REQUIRED*
Access to the repository requires another (separate) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a&nbsp;CVS repository password.*{color}

To do this, access the MBARI network (_usually through a command prompt, Cygwin window, or Linux terminal_)&nbsp;, telnet and login to moonjelly with your MBARI password.&nbsp;&nbsp;Next, type the&nbsp; following at the prompt: {color:red}{*}encryptCVSpw{*}{color}

This runs a script that outputs an encrypted version of your password.

{color:#ff0000}{*}+\!\!\! Please e-mail me the encrypted text (exactly as shown) so{+}{*}{color} {color:#ff0000}{*}{+}that I may add you to the repository password list. I will{+}{*}{color} {color:#ff0000}{*}{+}send you an e-mail when you are able to access the repository. \!\!\!+{*}{color} \\

*CVS GUIs*
GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2"&nbsp;link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here:
[http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .&nbsp;
{color:black}This will allow you to simply read any of the project modules.&nbsp;{color} Let me know how it works and if you have any problems. In addition,

Please&nbsp;remember to&nbsp;e-mail your encrypted password as soon as possible to me at: salamy@mbari.org.\\

Regards, - *Karen A. Salamy* (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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<property name="body"><![CDATA[----
&nbsp;
*Welcome to CVS\!*&nbsp; CVS is the MBARI Software Engineering source code repository which resides on the Linux server 'moonjelly'.&nbsp; You have requested to be added to the module called "ESP" in the CVS repository.&nbsp; You have been given access to the *"ESP"*, and "*cvs*" modules (projects).&nbsp; As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} is one of these two. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly.

*PERMISSIONS*
Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. moonjelly is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot for any reason, please let me know.
&nbsp;

*PASSWORD ACCESS REQUIRED*
Access to the repository requires another (separate) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network, telnet and login to moonjelly and type the&nbsp; following at the prompt: {color:red}{*}encryptCVSpw{*}{color}

This runs a script that outputs an encrypted version of your password.

*+\!\!\! Please e-mail me the encrypted text (exactly as shown) so{+}* *{+}that I may add you to the repository password list. I will{+}* *{+}send you an e-mail when you are able to access the repository. \!\!\!+*
\\

*CVS GUIs*
GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2"&nbsp;link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here:
[http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .&nbsp;
{color:black}This will allow you to simply read any of the project modules.&nbsp;{color} Let me know how it works and if you have any problems. In addition,

*PLEASE* remember to send me your encrypted password as soon as possible.
&nbsp;
Regards, - *Karen A. Salamy* (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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<property name="body"><![CDATA[----
*Welcome to CVS\!*&nbsp; CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp; You have requested to be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).

\\
\\
\\
&nbsp;

*PERMISSIONS*
Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. _moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot for any reason, please let me know.

\\
\\
&nbsp;

*PASSWORD ACCESS REQUIRED*
Access to the repository requires another (separate) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a&nbsp;CVS repository password.*{color}

To do this, access the MBARI network (_usually through a command prompt, Cygwin window, or Linux terminal_)&nbsp;, telnet and login to moonjelly with your MBARI password.&nbsp;&nbsp;Next, type the&nbsp; following at the prompt: {color:red}{*}encryptCVSpw{*}{color}

This runs a script that outputs an encrypted version of your password.

{color:#ff0000}{*}+\!\!\! Please e-mail me the encrypted text (exactly as shown) so{+}{*}{color} {color:#ff0000}{*}{+}that I may add you to the repository password list. I will{+}{*}{color} {color:#ff0000}{*}{+}send you an e-mail when you are able to access the repository. \!\!\!+{*}{color}

\\
\\
&nbsp;

*CVS GUIs*
GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2"&nbsp;link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here:
[http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .&nbsp;
{color:black}This will allow you to simply read any of the project modules.&nbsp;{color} Let me know how it works and if you have any problems. In addition,

Please&nbsp;remember to&nbsp;e-mail your encrypted password as soon as possible to me at: salamy@mbari.org.
\\

\\
&nbsp;

Regards, - *Karen A. Salamy* (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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<property name="body"><![CDATA[----
*Welcome to CVS\!*&nbsp; CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp; You have requested to be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\
\\ \\

*PERMISSIONS*
Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. _moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot for any reason, please let me know.
\\
\\

*PASSWORD ACCESS REQUIRED*
Access to the repository requires another (separate) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a&nbsp;CVS repository password.*{color}

To do this, access the MBARI network (_usually through a command prompt, Cygwin window, or Linux terminal_)&nbsp;, telnet and login to moonjelly with your MBARI password.&nbsp;&nbsp;Next, type the&nbsp; following at the prompt: {color:red}{*}encryptCVSpw{*}{color}

This runs a script that outputs an encrypted version of your password.

{color:#ff0000}{*}+\!\!\! Please e-mail me the encrypted text (exactly as shown) so{+}{*}{color} {color:#ff0000}{*}{+}that I may add you to the repository password list. I will{+}{*}{color} {color:#ff0000}{*}{+}send you an e-mail when you are able to access the repository. \!\!\!+{*}{color}
\\ \\

*CVS GUIs*
GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2"&nbsp;link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here:
[http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .&nbsp;
{color:black}This will allow you to simply read any of the project modules.&nbsp;{color} Let me know how it works and if you have any problems. In addition,

Please&nbsp;remember to&nbsp;e-mail your encrypted password as soon as possible to me at: salamy@mbari.org.
\\

\\
&nbsp;

Regards, - *Karen A. Salamy* (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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<property name="body"><![CDATA[h2. Adding your code to MBARI's repository

Here's the standard method of adding a new directory to the subversion repository.

1) On your local machine create the following directory structure
{noformat}
tempdir
`~~ myproject       <-- Replace 'myproject' with the name of your project
   `~~ tags
   `~~ branches
   `~~ trunk
      `~~ agent
      `~~ ctd2007
{noformat}

2) cd to _tempdir_ and run the following command
{{svn import myproject svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject}}

3) To check out _myproject's_ main trunk on another machine you run the command
{{svn co svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject/trunk myproject}}
{note:title=Be Careful}
Notice that we've added '/trunk' to the SVN URL above to check out only the trunk (main development line). If you omit '/trunk' you will check out all tags and branches as well as the trunk.
{note}

A free on-line guide to SVN is available at http://svnbook.red-bean.com/. The most useful svn commands are

{noformat}
svn status                            <-- shows you the status of files in your project
svn add some/new/file                 <-- add a new file to version control
svn del some/old/file                 <-- remove a file from version control
svn update                            <-- Get changes from the repository 
svn commit -m "some commit message"   <-- commit changes to the repository
svn help
{noformat}

If you find that you can't connect to the svn repository contact Karen Salamy. She may need to give you access permissions.
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms.  http://www.act-us.info/
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. www.alfresco.com
# ALOHA-MARS: http://alohamooring.apl.washington.edu/ ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of ~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). http://seahurst.apl.washington.edu/mars.php
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection http://www.mbari.org/aved/
# AWW: All was well. http://www.jkrowling.com/en/
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System http://www.mbari.org/expeditions/Pulse53/gear.htm
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology http://en.wikipedia.org/wiki/Caltech  
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure http://en.wikipedia.org/wiki/Cyberinfrastructure
# CeNCOOS: Central and Northern California Ocean Observing System http://www.cencoos.org/ 
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine http://www.webopedia.com/TERM/C/CNAME.htm 
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison http://www.cs.wisc.edu/condor/
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. http://www.unixgeeks.org/security/newbie/unix/cron-1.html 
# CTD: Conductivity, Temperature, and Depth http://www.whoi.edu/instruments/viewInstrument.do?id=1003
# CVS: Concurrent Versions System; maintains control of history of code/documents 
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. http://en.wikipedia.org/wiki/Demilitarized_zone_(computing) 
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering 
# eGY: the Electronic Geophysical Year http://www.egy.org/
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring.  http://www.mbari.org/mars/general/eits.html
# EOM: Electro-Optical-Mechanical
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network
# ESP: Environmental Sample Processor - Chris Scholin et al. http://www.mbari.org/muse/platforms/ESP.htm
## Darlene was the 1st generation ESP 
## GiGi The first 'second generation' ESP instrument 
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument 
## Bruce Another 'third generation' ESP instrument 
## MOE A third gen. instrument with the MFB connected 
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer 
# GEOSS: Global Earth Observation System of Systems http://www.epa.gov/geoss/
# GUI: Graphical User Interface 
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program 
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces 
# IDE: Integrated Development Environment      
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C++ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See http://www.iode.org/index.php?option=com_content&task=view&id=74 for details.
# IO: Implementing Organization www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf
# IOC: Intergovernmental Oceanographic Commission, http://ioc.unesco.org/iocweb/index.php
# IODE: International Oceanographic Data Exchange, www.iode.org
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, http://ioc.unesco.org/iocweb/index.php
# JIRA: A bug tracking, issue tracking, and project management application http://www.atlassian.com/software/jira/
# JOI: Joint Oceanographic Institutions http://www.joiscience.org/joi
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode 
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap 
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool.  http://maven.apache.org/
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). (http://marinemetadata.org/meta-t )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP 
# MMI: Marine Metadata Initiative http://marinemetadata.org/
# MOBB: Monterey Ocean Bottom Broadband project 
# Modbus: a serial communications protocol http://en.wikipedia.org/wiki/Modbus
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. http://mule.codehaus.org/display/MULE/Home
# MV: Medium Voltage (converter); located in node power supply of MARS 
# Nagios: software to monitor all types of computer and network services. http://www.nagios.org/
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form)             http://www.unidata.ucar.edu/software/netcdf/conventions.html
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. http://www.opengeospatial.org/
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. http://www.ogf.org/
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF)
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. http://www.oostethys.org/
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) http://www.pc104.org
# PCA: Principal component analysis. http://en.wikipedia.org/wiki/Principal_components_analysis
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?") 
# pH: a measure of the acidity or alkalinity of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. http://en.wikipedia.org/wiki/PH
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor". 
# PRDK: PUCK Reference Design Kit
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives http://en.wikipedia.org/wiki/RAID
# RBI: Runs Batted In
# RC: Radio controlled (airplane) 
# RCO: Regional Cabled Observatory http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems http://www.rosys.com/
# ROV: Remotely Operated Vehicle 
# RS-232 (Recommended Standard 232) is a standard for serial binary data signals connecting between a DTE (Data terminal equipment) and a DCE (Data Circuit-terminating Equipment). It is commonly used in computer serial ports. http://en.wikipedia.org/wiki/RS-232
# RSN: Regional Scale Node. See RCO. http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. (http://www.seadatanet.org/)
# SensorML: not an acronym; markup language to describe sensors and their data. http://vast.uah.edu/SensorML/  
# SIFT: Scale-invariant feature transform http://en.wikipedia.org/wiki/Scale-invariant_feature_transform
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module 
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/]  [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) http://www.tsa.gov/what_we_do/layers/twic/index.shtm
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of computer hardware that translates data between parallel and serial interfaces. http://en.wikipedia.org/wiki/UART
# UCB: University of California-Berkeley 
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of 61 academic institutions and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply 
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. http://www.venus.uvic.ca/
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language 
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, www.wmo.ch
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language http://en.wikipedia.org/wiki/XML
# XSD -- XML Schema Definition http://en.wikipedia.org/wiki/XML_Schema
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms.  http://www.act-us.info/
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# Alfresco: not an acronym. Open source content management system. www.alfresco.com
# ALOHA-MARS: http://alohamooring.apl.washington.edu/ ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of ~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). http://seahurst.apl.washington.edu/mars.php
# AMC: Autonomous Mission Controller
# APL: Applied Physics Laboratory, University of Washington
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection http://www.mbari.org/aved/
# AWW: All was well. http://www.jkrowling.com/en/
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# Bogey: not an acronym. A score of one over par on any individual hole.
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System http://www.mbari.org/expeditions/Pulse53/gear.htm
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology http://en.wikipedia.org/wiki/Caltech  
# CI: Cyberinfrastructure http://en.wikipedia.org/wiki/Cyberinfrastructure
# CeNCOOS: Central and Northern California Ocean Observing System http://www.cencoos.org/ 
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine http://www.webopedia.com/TERM/C/CNAME.htm 
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison http://www.cs.wisc.edu/condor/
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. http://www.unixgeeks.org/security/newbie/unix/cron-1.html 
# CTD: Conductivity, Temperature, and Depth http://www.whoi.edu/instruments/viewInstrument.do?id=1003
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DMZ: Demarcation zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. http://en.wikipedia.org/wiki/Demilitarized_zone_(computing) 
# eGY: the Electronic Geophysical Year http://www.egy.org/
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring.  http://www.mbari.org/mars/general/eits.html
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESP: Environmental Sample Processor - Chris Scholin et al. http://www.mbari.org/muse/platforms/ESP.htm
# Et al.: and others
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# GEOSS: Global Earth Observation System of Systems http://www.epa.gov/geoss/
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C++ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See http://www.iode.org/index.php?option=com_content&task=view&id=74 for details.
# IO: Implementing Organization www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf
# IOC: Intergovernmental Oceanographic Commission, http://ioc.unesco.org/iocweb/index.php
# IODE: International Oceanographic Data Exchange, www.iode.org
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, http://ioc.unesco.org/iocweb/index.php
# JIRA: A bug tracking, issue tracking, and project management application http://www.atlassian.com/software/jira/
# JOI: Joint Oceanographic Institutions http://www.joiscience.org/joi
# KML -- a file format used to display geographic data in an Earth browser, such as Google Earth
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool.  http://maven.apache.org/
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). (http://marinemetadata.org/meta-t )
# MMI: Marine Metadata Initiative http://marinemetadata.org/
# Modbus: a serial communications protocol http://en.wikipedia.org/wiki/Modbus
# Mule: not an acronym. Open source ESB. http://mule.codehaus.org/display/MULE/Home
# Nagios: software to monitor all types of computer and network services. http://www.nagios.org/
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form)             http://www.unidata.ucar.edu/software/netcdf/conventions.html
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# OBIS: Ocean Biogeographic Information System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. http://www.opengeospatial.org/
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. http://www.ogf.org/
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# OOI: Ocean Observatories Initiative (NSF)
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. http://www.oostethys.org/
# PC-104: small microprocessor for embedded systems (can run Linux) http://www.pc104.org
# PCA: Principal component analysis. http://en.wikipedia.org/wiki/Principal_components_analysis
# PCR: Polymerase Chain Reaction, a method of amplifying a DNA sample
# pH: a measure of the acidity or alkalinity of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. http://en.wikipedia.org/wiki/PH
# PDR: preliminary design review
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor". 
# PUP: Precision Underwater Positioner
# RAID: Redundant Array of Independent Drives http://en.wikipedia.org/wiki/RAID
# RBI: Runs Batted In
# RCO: Regional Cabled Observatory http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems http://www.rosys.com/
# RS-232 (Recommended Standard 232) is a standard for serial binary data signals connecting between a DTE (Data terminal equipment) and a DCE (Data Circuit-terminating Equipment). It is commonly used in computer serial ports. http://en.wikipedia.org/wiki/RS-232
# RSN: Regional Scale Node. See RCO. http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. (http://www.seadatanet.org/)
# SensorML: not an acronym; markup language to describe sensors and their data. http://vast.uah.edu/SensorML/  
# SIFT: Scale-invariant feature transform http://en.wikipedia.org/wiki/Scale-invariant_feature_transform
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision http://www.smdhydrovision.com/
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission http://www.sopac.org
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System http://www.mbari.org/ssds/  http://new-ssds.mbari.org:8080/ssds/
# SURA: The Southeastern Universities Research Association
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) http://www.tsa.gov/what_we_do/layers/twic/index.shtm
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of computer hardware that translates data between parallel and serial interfaces. http://en.wikipedia.org/wiki/UART
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of 61 academic institutions and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UW: University of Washington
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. http://www.venus.uvic.ca/
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WMO: World Meteorology Organization, www.wmo.ch
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language http://en.wikipedia.org/wiki/XML
# XSD -- XML Schema Definition http://en.wikipedia.org/wiki/XML_Schema]]></property>
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<property name="body"><![CDATA[h2.


----
*[*Welcome to CVS\!*|http://oceana:8081/display/CLT/Welcome+to+CVS%21]*

*[*Setting up a CVS Graphical User Interface (GUI)*|http://oceana:8081/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]**&nbsp;&nbsp;* *[*(Download .doc)*|CLT:CVS Client Software Downloads^Setting up WinCVS_1.2_new.doc]*

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator (_Karen Salamy:&nbsp;_ salamy@mbari.org). Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms.  http://www.act-us.info/
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. www.alfresco.com
# ALOHA-MARS: http://alohamooring.apl.washington.edu/ ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of ~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). http://seahurst.apl.washington.edu/mars.php
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection http://www.mbari.org/aved/
# AWW: All was well. http://www.jkrowling.com/en/
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System http://www.mbari.org/expeditions/Pulse53/gear.htm
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology http://en.wikipedia.org/wiki/Caltech  
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure http://en.wikipedia.org/wiki/Cyberinfrastructure
# CeNCOOS: Central and Northern California Ocean Observing System http://www.cencoos.org/ 
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine http://www.webopedia.com/TERM/C/CNAME.htm 
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison http://www.cs.wisc.edu/condor/
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. http://www.unixgeeks.org/security/newbie/unix/cron-1.html 
# CTD: Conductivity, Temperature, and Depth http://www.whoi.edu/instruments/viewInstrument.do?id=1003
# CVS: Concurrent Versions System; maintains control of history of code/documents 
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. http://en.wikipedia.org/wiki/Demilitarized_zone_(computing) 
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering 
# eGY: the Electronic Geophysical Year http://www.egy.org/
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring.  http://www.mbari.org/mars/general/eits.html
# EOM: Electro-Optical-Mechanical
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network http://www.oceanlab.abdn.ac.uk/research/esonet.php
# ESP: Environmental Sample Processor - Chris Scholin et al. http://www.mbari.org/muse/platforms/ESP.htm
## Darlene was the 1st generation ESP 
## GiGi The first 'second generation' ESP instrument 
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument 
## Bruce Another 'third generation' ESP instrument 
## MOE A third gen. instrument with the MFB connected 
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer 
# GEOSS: Global Earth Observation System of Systems http://www.epa.gov/geoss/
# GUI: Graphical User Interface 
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program 
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces 
# IDE: Integrated Development Environment      
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C++ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See http://www.iode.org/index.php?option=com_content&task=view&id=74 for details.
# IO: Implementing Organization www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf
# IOC: Intergovernmental Oceanographic Commission, http://ioc.unesco.org/iocweb/index.php
# IODE: International Oceanographic Data Exchange, www.iode.org
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, http://ioc.unesco.org/iocweb/index.php
# JIRA: A bug tracking, issue tracking, and project management application http://www.atlassian.com/software/jira/
# JOI: Joint Oceanographic Institutions http://www.joiscience.org/joi
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode 
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap 
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool.  http://maven.apache.org/
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). (http://marinemetadata.org/meta-t )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP 
# MMI: Marine Metadata Initiative http://marinemetadata.org/
# MOBB: Monterey Ocean Bottom Broadband project 
# Modbus: a serial communications protocol http://en.wikipedia.org/wiki/Modbus
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. http://mule.codehaus.org/display/MULE/Home
# MV: Medium Voltage (converter); located in node power supply of MARS 
# Nagios: software to monitor all types of computer and network services. http://www.nagios.org/
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form)             http://www.unidata.ucar.edu/software/netcdf/conventions.html
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. http://www.opengeospatial.org/
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. http://www.ogf.org/
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. http://www.oostethys.org/
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) http://www.pc104.org
# PCA: Principal component analysis. http://en.wikipedia.org/wiki/Principal_components_analysis
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?") 
# pH: a measure of the acidity or alkalinity of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. http://en.wikipedia.org/wiki/PH
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor". 
# PRDK: PUCK Reference Design Kit
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives http://en.wikipedia.org/wiki/RAID
# RBI: Runs Batted In
# RC: Radio controlled (airplane) 
# RCO: Regional Cabled Observatory http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems http://www.rosys.com/
# ROV: Remotely Operated Vehicle 
# RS-232 (Recommended Standard 232) is a standard for serial binary data signals connecting between a DTE (Data terminal equipment) and a DCE (Data Circuit-terminating Equipment). It is commonly used in computer serial ports. http://en.wikipedia.org/wiki/RS-232
# RSN: Regional Scale Node. See RCO. http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. (http://www.seadatanet.org/)
# SensorML: not an acronym; markup language to describe sensors and their data. http://vast.uah.edu/SensorML/  
# SIFT: Scale-invariant feature transform http://en.wikipedia.org/wiki/Scale-invariant_feature_transform
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module 
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/]  [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) http://www.tsa.gov/what_we_do/layers/twic/index.shtm
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of computer hardware that translates data between parallel and serial interfaces. http://en.wikipedia.org/wiki/UART
# UCB: University of California-Berkeley 
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of 61 academic institutions and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply 
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. http://www.venus.uvic.ca/
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language 
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, www.wmo.ch
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language http://en.wikipedia.org/wiki/XML
# XSD -- XML Schema Definition http://en.wikipedia.org/wiki/XML_Schema
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<property name="body"><![CDATA[h2.


----
*[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21]*

*[*\*Setting up a CVS Graphical User Interface (GUI)\**|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]**&nbsp;&nbsp;* *[*(Download .doc)*|CLT:CVS Client Software Downloads^Setting up WinCVS_1.2_new.doc]*

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator (_Karen Salamy:&nbsp;_ salamy@mbari.org). Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms.  http://www.act-us.info/
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. www.alfresco.com
# ALOHA-MARS: http://alohamooring.apl.washington.edu/ ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of ~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). http://seahurst.apl.washington.edu/mars.php
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection http://www.mbari.org/aved/
# AWW: All was well. http://www.jkrowling.com/en/
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System http://www.mbari.org/expeditions/Pulse53/gear.htm
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology http://en.wikipedia.org/wiki/Caltech  
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure http://en.wikipedia.org/wiki/Cyberinfrastructure
# CeNCOOS: Central and Northern California Ocean Observing System http://www.cencoos.org/ 
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine http://www.webopedia.com/TERM/C/CNAME.htm 
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison http://www.cs.wisc.edu/condor/
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. http://www.unixgeeks.org/security/newbie/unix/cron-1.html 
# CTD: Conductivity, Temperature, and Depth http://www.whoi.edu/instruments/viewInstrument.do?id=1003
# CVS: Concurrent Versions System; maintains control of history of code/documents 
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. http://en.wikipedia.org/wiki/Demilitarized_zone_(computing) 
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering 
# eGY: the Electronic Geophysical Year http://www.egy.org/
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring.  http://www.mbari.org/mars/general/eits.html
# EOM: Electro-Optical-Mechanical
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network http://www.oceanlab.abdn.ac.uk/research/esonet.php
# ESP: Environmental Sample Processor - Chris Scholin et al. http://www.mbari.org/muse/platforms/ESP.htm
## Darlene was the 1st generation ESP 
## GiGi The first 'second generation' ESP instrument 
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument 
## Bruce Another 'third generation' ESP instrument 
## MOE A third gen. instrument with the MFB connected 
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer 
# GEOSS: Global Earth Observation System of Systems http://www.epa.gov/geoss/
# GUI: Graphical User Interface 
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program 
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces 
# IDE: Integrated Development Environment      
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C++ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See http://www.iode.org/index.php?option=com_content&task=view&id=74 for details.
# IO: Implementing Organization www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf
# IOC: Intergovernmental Oceanographic Commission, http://ioc.unesco.org/iocweb/index.php
# IODE: International Oceanographic Data Exchange, www.iode.org
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, http://ioc.unesco.org/iocweb/index.php
# JIRA: A bug tracking, issue tracking, and project management application http://www.atlassian.com/software/jira/
# JOI: Joint Oceanographic Institutions http://www.joiscience.org/joi
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode 
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap 
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool.  http://maven.apache.org/
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). (http://marinemetadata.org/meta-t )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP 
# MMI: Marine Metadata Initiative http://marinemetadata.org/
# MOBB: Monterey Ocean Bottom Broadband project 
# Modbus: a serial communications protocol http://en.wikipedia.org/wiki/Modbus
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. http://mule.codehaus.org/display/MULE/Home
# MV: Medium Voltage (converter); located in node power supply of MARS 
# Nagios: software to monitor all types of computer and network services. http://www.nagios.org/
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form)             http://www.unidata.ucar.edu/software/netcdf/conventions.html
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. http://www.opengeospatial.org/
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. http://www.ogf.org/
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF)
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. http://www.oostethys.org/
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) http://www.pc104.org
# PCA: Principal component analysis. http://en.wikipedia.org/wiki/Principal_components_analysis
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?") 
# pH: a measure of the acidity or alkalinity of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. http://en.wikipedia.org/wiki/PH
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor". 
# PRDK: PUCK Reference Design Kit
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives http://en.wikipedia.org/wiki/RAID
# RBI: Runs Batted In
# RC: Radio controlled (airplane) 
# RCO: Regional Cabled Observatory http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems http://www.rosys.com/
# ROV: Remotely Operated Vehicle 
# RS-232 (Recommended Standard 232) is a standard for serial binary data signals connecting between a DTE (Data terminal equipment) and a DCE (Data Circuit-terminating Equipment). It is commonly used in computer serial ports. http://en.wikipedia.org/wiki/RS-232
# RSN: Regional Scale Node. See RCO. http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. (http://www.seadatanet.org/)
# SensorML: not an acronym; markup language to describe sensors and their data. http://vast.uah.edu/SensorML/  
# SIFT: Scale-invariant feature transform http://en.wikipedia.org/wiki/Scale-invariant_feature_transform
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module 
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/]  [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) http://www.tsa.gov/what_we_do/layers/twic/index.shtm
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of computer hardware that translates data between parallel and serial interfaces. http://en.wikipedia.org/wiki/UART
# UCB: University of California-Berkeley 
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of 61 academic institutions and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply 
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. http://www.venus.uvic.ca/
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language 
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, www.wmo.ch
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language http://en.wikipedia.org/wiki/XML
# XSD -- XML Schema Definition http://en.wikipedia.org/wiki/XML_Schema
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms.  http://www.act-us.info/
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. www.alfresco.com
# ALOHA-MARS: http://alohamooring.apl.washington.edu/ ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of ~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). http://seahurst.apl.washington.edu/mars.php
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection http://www.mbari.org/aved/
# AWW: All was well. http://www.jkrowling.com/en/
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System http://www.mbari.org/expeditions/Pulse53/gear.htm
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology http://en.wikipedia.org/wiki/Caltech  
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure http://en.wikipedia.org/wiki/Cyberinfrastructure
# CeNCOOS: Central and Northern California Ocean Observing System http://www.cencoos.org/ 
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine http://www.webopedia.com/TERM/C/CNAME.htm 
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison http://www.cs.wisc.edu/condor/
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. http://www.unixgeeks.org/security/newbie/unix/cron-1.html 
# CTD: Conductivity, Temperature, and Depth http://www.whoi.edu/instruments/viewInstrument.do?id=1003
# CVS: Concurrent Versions System; maintains control of history of code/documents 
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. http://en.wikipedia.org/wiki/Demilitarized_zone_(computing) 
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering 
# eGY: the Electronic Geophysical Year http://www.egy.org/
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring.  http://www.mbari.org/mars/general/eits.html
# EOM: Electro-Optical-Mechanical
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network http://www.oceanlab.abdn.ac.uk/research/esonet.php
# ESP: Environmental Sample Processor - Chris Scholin et al. http://www.mbari.org/muse/platforms/ESP.htm
## Darlene was the 1st generation ESP 
## GiGi The first 'second generation' ESP instrument 
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument 
## Bruce Another 'third generation' ESP instrument 
## MOE A third gen. instrument with the MFB connected 
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer 
# GEOSS: Global Earth Observation System of Systems http://www.epa.gov/geoss/
# GUI: Graphical User Interface 
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program 
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces 
# IDE: Integrated Development Environment      
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C++ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See http://www.iode.org/index.php?option=com_content&task=view&id=74 for details.
# IO: Implementing Organization www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf
# IOC: Intergovernmental Oceanographic Commission, http://ioc.unesco.org/iocweb/index.php
# IODE: International Oceanographic Data Exchange, www.iode.org
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, http://ioc.unesco.org/iocweb/index.php
# JIRA: A bug tracking, issue tracking, and project management application http://www.atlassian.com/software/jira/
# JOI: Joint Oceanographic Institutions http://www.joiscience.org/joi
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode 
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap 
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool.  http://maven.apache.org/
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). (http://marinemetadata.org/meta-t )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP 
# MMI: Marine Metadata Initiative http://marinemetadata.org/
# MOBB: Monterey Ocean Bottom Broadband project 
# Modbus: a serial communications protocol http://en.wikipedia.org/wiki/Modbus
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. http://mule.codehaus.org/display/MULE/Home
# MV: Medium Voltage (converter); located in node power supply of MARS 
# Nagios: software to monitor all types of computer and network services. http://www.nagios.org/
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form)             http://www.unidata.ucar.edu/software/netcdf/conventions.html
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. http://www.opengeospatial.org/
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. http://www.ogf.org/
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF)
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. http://www.oostethys.org/
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) http://www.pc104.org
# PCA: Principal component analysis. http://en.wikipedia.org/wiki/Principal_components_analysis
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?") 
# pH: a measure of the acidity or alkalinity of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. http://en.wikipedia.org/wiki/PH
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor". 
# PRDK: PUCK Reference Design Kit
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives http://en.wikipedia.org/wiki/RAID
# RBI: Runs Batted In
# RC: Radio controlled (airplane) 
# RCO: Regional Cabled Observatory http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems http://www.rosys.com/
# ROV: Remotely Operated Vehicle 
# RS-232 (Recommended Standard 232) is a standard for serial binary data signals connecting between a DTE (Data terminal equipment) and a DCE (Data Circuit-terminating Equipment). It is commonly used in computer serial ports. http://en.wikipedia.org/wiki/RS-232
# RSN: Regional Scale Node. See RCO. http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. (http://www.seadatanet.org/)
# SensorML: not an acronym; markup language to describe sensors and their data. http://vast.uah.edu/SensorML/  
# SIFT: Scale-invariant feature transform http://en.wikipedia.org/wiki/Scale-invariant_feature_transform
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module 
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/]  [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) http://www.tsa.gov/what_we_do/layers/twic/index.shtm
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of computer hardware that translates data between parallel and serial interfaces. http://en.wikipedia.org/wiki/UART
# UCB: University of California-Berkeley 
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of 61 academic institutions and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply 
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. http://www.venus.uvic.ca/
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language 
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, www.wmo.ch
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language http://en.wikipedia.org/wiki/XML
# XSD -- XML Schema Definition http://en.wikipedia.org/wiki/XML_Schema
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms.  http://www.act-us.info/
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. http://www.alfresco.com http://alfresco.mbari.org
# ALOHA-MARS: http://alohamooring.apl.washington.edu/ ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of ~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). http://seahurst.apl.washington.edu/mars.php
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection http://www.mbari.org/aved/
# AWW: All was well. http://www.jkrowling.com/en/
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System http://www.mbari.org/expeditions/Pulse53/gear.htm
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology http://en.wikipedia.org/wiki/Caltech  
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure http://en.wikipedia.org/wiki/Cyberinfrastructure
# CeNCOOS: Central and Northern California Ocean Observing System http://www.cencoos.org/ 
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine http://www.webopedia.com/TERM/C/CNAME.htm 
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison http://www.cs.wisc.edu/condor/
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. http://www.unixgeeks.org/security/newbie/unix/cron-1.html 
# CTD: Conductivity, Temperature, and Depth http://www.whoi.edu/instruments/viewInstrument.do?id=1003
# CVS: Concurrent Versions System; maintains control of history of code/documents 
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. http://en.wikipedia.org/wiki/Demilitarized_zone_(computing) 
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering 
# eGY: the Electronic Geophysical Year http://www.egy.org/
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring.  http://www.mbari.org/mars/general/eits.html
# EOM: Electro-Optical-Mechanical
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network http://www.oceanlab.abdn.ac.uk/research/esonet.php
# ESP: Environmental Sample Processor - Chris Scholin et al. http://www.mbari.org/muse/platforms/ESP.htm
## Darlene was the 1st generation ESP 
## GiGi The first 'second generation' ESP instrument 
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument 
## Bruce Another 'third generation' ESP instrument 
## MOE A third gen. instrument with the MFB connected 
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer 
# GEOSS: Global Earth Observation System of Systems http://www.epa.gov/geoss/
# GUI: Graphical User Interface 
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program 
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces 
# IDE: Integrated Development Environment      
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C++ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See http://www.iode.org/index.php?option=com_content&task=view&id=74 for details.
# IO: Implementing Organization http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf
# IOC: Intergovernmental Oceanographic Commission, http://ioc.unesco.org/iocweb/index.php
# IODE: International Oceanographic Data Exchange, http://www.iode.org
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, http://ioc.unesco.org/iocweb/index.php
# JIRA: A bug tracking, issue tracking, and project management application http://www.atlassian.com/software/jira/
# JOI: Joint Oceanographic Institutions http://www.joiscience.org/joi
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode 
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap 
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool.  http://maven.apache.org/
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). (http://marinemetadata.org/meta-t )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP 
# MMI: Marine Metadata Initiative http://marinemetadata.org/
# MOBB: Monterey Ocean Bottom Broadband project 
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] http://en.wikipedia.org/wiki/Modbus
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. http://mule.codehaus.org/display/MULE/Home
# MV: Medium Voltage (converter); located in node power supply of MARS 
# Nagios: software to monitor all types of computer and network services. http://www.nagios.org/
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form)             http://www.unidata.ucar.edu/software/netcdf/conventions.html
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. http://www.opengeospatial.org/
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. http://www.ogf.org/
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. http://www.oostethys.org/
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) http://www.pc104.org
# PCA: Principal component analysis. http://en.wikipedia.org/wiki/Principal_components_analysis
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?") 
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. http://en.wikipedia.org/wiki/PH
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor". 
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives http://en.wikipedia.org/wiki/RAID
# RBI: Runs Batted In
# RC: Radio controlled (airplane) 
# RCO: Regional Cabled Observatory http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems http://www.rosys.com/
# ROV: Remotely Operated Vehicle 
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. http://en.wikipedia.org/wiki/RS-232
# RSN: Regional Scale Node. See RCO. http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. (http://www.seadatanet.org/)
# SensorML: not an acronym; markup language to describe sensors and their data. http://vast.uah.edu/SensorML/  
# SIFT: Scale-invariant feature transform http://en.wikipedia.org/wiki/Scale-invariant_feature_transform
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module 
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/]  [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) http://www.tsa.gov/what_we_do/layers/twic/index.shtm
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of computer hardware that translates data between parallel and serial interfaces. http://en.wikipedia.org/wiki/UART
# UCB: University of California-Berkeley 
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of 61 academic institutions and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply 
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. http://www.venus.uvic.ca/
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language 
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, www.wmo.ch
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language http://en.wikipedia.org/wiki/XML
# XSD -- XML Schema Definition http://en.wikipedia.org/wiki/XML_Schema
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h3. *Setting up WinCVS (v. 1.2) on your Windows 2000/XP (x86) computer to access the MBARI&nbsp;*{*}{_}moonjelly{_}* *CVS source code repository.*&nbsp;

*1).* To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;https://oceana.mbari.org/confluence/display/~salamy/Helpful+Software+Downloads and copy&nbsp;the *{_}WinCVS-1.2.0.zip{_}* folder to your Desktop.&nbsp; Extract all files to your *{_}C:\Program_Files{_}*&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
*2).* Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as *{_}C:\Program_Files\GNU\WinCVS_1.2{_}* .

\\
*3).*&nbsp;Once installed, open WinCVS (*{_}Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS{_}*).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says *"ENTER THE CVSROOT"* .&nbsp; An example of this would be (_salamy@moonjelly:/home/cvs_) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the *"AUTHENTIFICATION:"* setting to - *_"passwd" file on the cvs server._*
* Finally, click the _WinCVS_ tab and set your *"home"* directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).
\\

\\
*&nbsp;4).*&nbsp;*NOTE:*&nbsp; To actually use this GUI on the moonjelly repository you will first need an excrypted CVS respository password (see also&nbsp;*"Password Access"* at the following link: [http://oceana:8081/display/CLT/Welcome+to+CVS%21]).
* To do this, telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command {color:#ff0000}{*}{+}encryptCVSpw{+}{*}{color}.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (\*_exactly as listed_\*) to the CVS&nbsp;administrator (*salamy@mbari.org). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.
\\
\\
\\

*5).*&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms.  http://www.act-us.info/
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. http://www.alfresco.com http://alfresco.mbari.org
# ALOHA-MARS: http://alohamooring.apl.washington.edu/ ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of ~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). http://seahurst.apl.washington.edu/mars.php
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection http://www.mbari.org/aved/
# AWW: All was well. http://www.jkrowling.com/en/
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System http://www.mbari.org/expeditions/Pulse53/gear.htm
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology http://en.wikipedia.org/wiki/Caltech  
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure http://en.wikipedia.org/wiki/Cyberinfrastructure
# CeNCOOS: Central and Northern California Ocean Observing System http://www.cencoos.org/ 
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine http://www.webopedia.com/TERM/C/CNAME.htm 
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison http://www.cs.wisc.edu/condor/
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. http://www.unixgeeks.org/security/newbie/unix/cron-1.html 
# CTD: Conductivity, Temperature, and Depth http://www.whoi.edu/instruments/viewInstrument.do?id=1003
# CVS: Concurrent Versions System; maintains control of history of code/documents 
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. http://en.wikipedia.org/wiki/Demilitarized_zone_(computing) 
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering 
# eGY: the Electronic Geophysical Year http://www.egy.org/
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring.  http://www.mbari.org/mars/general/eits.html
# EOM: Electro-Optical-Mechanical
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network http://www.oceanlab.abdn.ac.uk/research/esonet.php
# ESP: Environmental Sample Processor - Chris Scholin et al. http://www.mbari.org/muse/platforms/ESP.htm
## Darlene was the 1st generation ESP 
## GiGi The first 'second generation' ESP instrument 
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument 
## Bruce Another 'third generation' ESP instrument 
## MOE A third gen. instrument with the MFB connected 
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer 
# GEOSS: Global Earth Observation System of Systems http://www.epa.gov/geoss/
# GUI: Graphical User Interface 
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program 
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces 
# IDE: Integrated Development Environment      
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C++ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See http://www.iode.org/index.php?option=com_content&task=view&id=74 for details.
# IO: Implementing Organization http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf
# IOC: Intergovernmental Oceanographic Commission, http://ioc.unesco.org/iocweb/index.php
# IODE: International Oceanographic Data Exchange, http://www.iode.org
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, http://ioc.unesco.org/iocweb/index.php
# JIRA: A bug tracking, issue tracking, and project management application http://www.atlassian.com/software/jira/
# JOI: Joint Oceanographic Institutions http://www.joiscience.org/joi
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode 
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap 
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool.  http://maven.apache.org/
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). (http://marinemetadata.org/meta-t )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP 
# MMI: Marine Metadata Initiative http://marinemetadata.org/
# MOBB: Monterey Ocean Bottom Broadband project 
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] http://en.wikipedia.org/wiki/Modbus
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. http://mule.codehaus.org/display/MULE/Home
# MV: Medium Voltage (converter); located in node power supply of MARS 
# Nagios: software to monitor all types of computer and network services. http://www.nagios.org/
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form)             http://www.unidata.ucar.edu/software/netcdf/conventions.html
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. http://www.opengeospatial.org/
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. http://www.ogf.org/
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. http://www.oostethys.org/
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) http://www.pc104.org
# PCA: Principal component analysis. http://en.wikipedia.org/wiki/Principal_components_analysis
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?") 
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. http://en.wikipedia.org/wiki/PH
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor". 
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives http://en.wikipedia.org/wiki/RAID
# RBI: Runs Batted In
# RC: Radio controlled (airplane) 
# RCO: Regional Cabled Observatory http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems http://www.rosys.com/
# ROV: Remotely Operated Vehicle 
# RS-232 (Recommended Standard 232) is a standard for serial binary data signals connecting between a DTE (Data terminal equipment) and a DCE (Data Circuit-terminating Equipment). It is commonly used in computer serial ports. http://en.wikipedia.org/wiki/RS-232
# RSN: Regional Scale Node. See RCO. http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. (http://www.seadatanet.org/)
# SensorML: not an acronym; markup language to describe sensors and their data. http://vast.uah.edu/SensorML/  
# SIFT: Scale-invariant feature transform http://en.wikipedia.org/wiki/Scale-invariant_feature_transform
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module 
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/]  [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) http://www.tsa.gov/what_we_do/layers/twic/index.shtm
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of computer hardware that translates data between parallel and serial interfaces. http://en.wikipedia.org/wiki/UART
# UCB: University of California-Berkeley 
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of 61 academic institutions and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply 
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. http://www.venus.uvic.ca/
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language 
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, www.wmo.ch
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language http://en.wikipedia.org/wiki/XML
# XSD -- XML Schema Definition http://en.wikipedia.org/wiki/XML_Schema
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<property name="body"><![CDATA[----
h3. *Setting up WinCVS (v. 1.2) on your Windows 2000/XP (x86) computer to access the MBARI&nbsp;*{*}{_}moonjelly{_}* *CVS source code repository.*&nbsp;

*1).* To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[https://oceana.mbari.org/confluence/display/~salamy/Helpful+Software+Downloads] and copy&nbsp;the *{_}WinCVS-1.2.0.zip{_}* folder to your Desktop.&nbsp; Extract all files to your *{_}C:\Program_Files{_}*&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
*2).* Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as *{_}C:\Program_Files\GNU\WinCVS_1.2{_}* .

\\
*3).*&nbsp;Once installed, open WinCVS (*{_}Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS{_}*).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says *"ENTER THE CVSROOT"* .&nbsp; An example of this would be (_salamy@moonjelly:/home/cvs_) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the *"AUTHENTIFICATION:"* setting to - *_"passwd" file on the cvs server._*
* Finally, click the _WinCVS_ tab and set your *"home"* directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).
\\

\\
*&nbsp;4).*&nbsp;*NOTE:*&nbsp; To actually use this GUI on the moonjelly repository you will first need an excrypted CVS respository password (see also&nbsp;*"Password Access"* at the following link: https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21
* To do this, telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command {color:#ff0000}{*}{+}encryptCVSpw{+}{*}{color}.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (\*_exactly as listed_\*) to the CVS&nbsp;administrator (*salamy@mbari.org). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.
\\
\\
\\

*5).*&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms.  http://www.act-us.info/
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. www.alfresco.com
# ALOHA-MARS: http://alohamooring.apl.washington.edu/ ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of ~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). http://seahurst.apl.washington.edu/mars.php
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection http://www.mbari.org/aved/
# AWW: All was well. http://www.jkrowling.com/en/
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System http://www.mbari.org/expeditions/Pulse53/gear.htm
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology http://en.wikipedia.org/wiki/Caltech  
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure http://en.wikipedia.org/wiki/Cyberinfrastructure
# CeNCOOS: Central and Northern California Ocean Observing System http://www.cencoos.org/ 
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine http://www.webopedia.com/TERM/C/CNAME.htm 
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison http://www.cs.wisc.edu/condor/
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. http://www.unixgeeks.org/security/newbie/unix/cron-1.html 
# CTD: Conductivity, Temperature, and Depth http://www.whoi.edu/instruments/viewInstrument.do?id=1003
# CVS: Concurrent Versions System; maintains control of history of code/documents 
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. http://en.wikipedia.org/wiki/Demilitarized_zone_(computing) 
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering 
# eGY: the Electronic Geophysical Year http://www.egy.org/
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring.  http://www.mbari.org/mars/general/eits.html
# EOM: Electro-Optical-Mechanical
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network http://www.oceanlab.abdn.ac.uk/research/esonet.php
# ESP: Environmental Sample Processor - Chris Scholin et al. http://www.mbari.org/muse/platforms/ESP.htm
## Darlene was the 1st generation ESP 
## GiGi The first 'second generation' ESP instrument 
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument 
## Bruce Another 'third generation' ESP instrument 
## MOE A third gen. instrument with the MFB connected 
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer 
# GEOSS: Global Earth Observation System of Systems http://www.epa.gov/geoss/
# GUI: Graphical User Interface 
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program 
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces 
# IDE: Integrated Development Environment      
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C++ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See http://www.iode.org/index.php?option=com_content&task=view&id=74 for details.
# IO: Implementing Organization http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf
# IOC: Intergovernmental Oceanographic Commission, http://ioc.unesco.org/iocweb/index.php
# IODE: International Oceanographic Data Exchange, www.iode.org
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, http://ioc.unesco.org/iocweb/index.php
# JIRA: A bug tracking, issue tracking, and project management application http://www.atlassian.com/software/jira/
# JOI: Joint Oceanographic Institutions http://www.joiscience.org/joi
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode 
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap 
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool.  http://maven.apache.org/
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). (http://marinemetadata.org/meta-t )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP 
# MMI: Marine Metadata Initiative http://marinemetadata.org/
# MOBB: Monterey Ocean Bottom Broadband project 
# Modbus: a serial communications protocol http://en.wikipedia.org/wiki/Modbus
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. http://mule.codehaus.org/display/MULE/Home
# MV: Medium Voltage (converter); located in node power supply of MARS 
# Nagios: software to monitor all types of computer and network services. http://www.nagios.org/
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form)             http://www.unidata.ucar.edu/software/netcdf/conventions.html
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. http://www.opengeospatial.org/
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. http://www.ogf.org/
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. http://www.oostethys.org/
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) http://www.pc104.org
# PCA: Principal component analysis. http://en.wikipedia.org/wiki/Principal_components_analysis
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?") 
# pH: a measure of the acidity or alkalinity of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. http://en.wikipedia.org/wiki/PH
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor". 
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives http://en.wikipedia.org/wiki/RAID
# RBI: Runs Batted In
# RC: Radio controlled (airplane) 
# RCO: Regional Cabled Observatory http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems http://www.rosys.com/
# ROV: Remotely Operated Vehicle 
# RS-232 (Recommended Standard 232) is a standard for serial binary data signals connecting between a DTE (Data terminal equipment) and a DCE (Data Circuit-terminating Equipment). It is commonly used in computer serial ports. http://en.wikipedia.org/wiki/RS-232
# RSN: Regional Scale Node. See RCO. http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. (http://www.seadatanet.org/)
# SensorML: not an acronym; markup language to describe sensors and their data. http://vast.uah.edu/SensorML/  
# SIFT: Scale-invariant feature transform http://en.wikipedia.org/wiki/Scale-invariant_feature_transform
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module 
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/]  [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) http://www.tsa.gov/what_we_do/layers/twic/index.shtm
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of computer hardware that translates data between parallel and serial interfaces. http://en.wikipedia.org/wiki/UART
# UCB: University of California-Berkeley 
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of 61 academic institutions and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply 
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. http://www.venus.uvic.ca/
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language 
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, www.wmo.ch
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language http://en.wikipedia.org/wiki/XML
# XSD -- XML Schema Definition http://en.wikipedia.org/wiki/XML_Schema
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms.  http://www.act-us.info/
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. http://www.alfresco.com http://alfresco.mbari.org
# ALOHA-MARS: http://alohamooring.apl.washington.edu/ ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of ~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). http://seahurst.apl.washington.edu/mars.php
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection http://www.mbari.org/aved/
# AWW: All was well. http://www.jkrowling.com/en/
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System http://www.mbari.org/expeditions/Pulse53/gear.htm
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology http://en.wikipedia.org/wiki/Caltech  
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure http://en.wikipedia.org/wiki/Cyberinfrastructure
# CeNCOOS: Central and Northern California Ocean Observing System http://www.cencoos.org/ 
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine http://www.webopedia.com/TERM/C/CNAME.htm 
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison http://www.cs.wisc.edu/condor/
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. http://www.unixgeeks.org/security/newbie/unix/cron-1.html 
# CTD: Conductivity, Temperature, and Depth http://www.whoi.edu/instruments/viewInstrument.do?id=1003
# CVS: Concurrent Versions System; maintains control of history of code/documents 
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. http://en.wikipedia.org/wiki/Demilitarized_zone_(computing) 
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering 
# eGY: the Electronic Geophysical Year http://www.egy.org/
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring.  http://www.mbari.org/mars/general/eits.html
# EOM: Electro-Optical-Mechanical
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network http://www.oceanlab.abdn.ac.uk/research/esonet.php
# ESP: Environmental Sample Processor - Chris Scholin et al. http://www.mbari.org/muse/platforms/ESP.htm
## Darlene was the 1st generation ESP 
## GiGi The first 'second generation' ESP instrument 
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument 
## Bruce Another 'third generation' ESP instrument 
## MOE A third gen. instrument with the MFB connected 
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer 
# GEOSS: Global Earth Observation System of Systems http://www.epa.gov/geoss/
# GUI: Graphical User Interface 
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program 
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces 
# IDE: Integrated Development Environment      
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C++ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See http://www.iode.org/index.php?option=com_content&task=view&id=74 for details.
# IO: Implementing Organization http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf
# IOC: Intergovernmental Oceanographic Commission, http://ioc.unesco.org/iocweb/index.php
# IODE: International Oceanographic Data Exchange, www.iode.org
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, http://ioc.unesco.org/iocweb/index.php
# JIRA: A bug tracking, issue tracking, and project management application http://www.atlassian.com/software/jira/
# JOI: Joint Oceanographic Institutions http://www.joiscience.org/joi
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode 
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap 
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool.  http://maven.apache.org/
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). (http://marinemetadata.org/meta-t )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP 
# MMI: Marine Metadata Initiative http://marinemetadata.org/
# MOBB: Monterey Ocean Bottom Broadband project 
# Modbus: a serial communications protocol http://en.wikipedia.org/wiki/Modbus
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. http://mule.codehaus.org/display/MULE/Home
# MV: Medium Voltage (converter); located in node power supply of MARS 
# Nagios: software to monitor all types of computer and network services. http://www.nagios.org/
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form)             http://www.unidata.ucar.edu/software/netcdf/conventions.html
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. http://www.opengeospatial.org/
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. http://www.ogf.org/
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. http://www.oostethys.org/
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) http://www.pc104.org
# PCA: Principal component analysis. http://en.wikipedia.org/wiki/Principal_components_analysis
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?") 
# pH: a measure of the acidity or alkalinity of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. http://en.wikipedia.org/wiki/PH
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor". 
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives http://en.wikipedia.org/wiki/RAID
# RBI: Runs Batted In
# RC: Radio controlled (airplane) 
# RCO: Regional Cabled Observatory http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems http://www.rosys.com/
# ROV: Remotely Operated Vehicle 
# RS-232 (Recommended Standard 232) is a standard for serial binary data signals connecting between a DTE (Data terminal equipment) and a DCE (Data Circuit-terminating Equipment). It is commonly used in computer serial ports. http://en.wikipedia.org/wiki/RS-232
# RSN: Regional Scale Node. See RCO. http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. (http://www.seadatanet.org/)
# SensorML: not an acronym; markup language to describe sensors and their data. http://vast.uah.edu/SensorML/  
# SIFT: Scale-invariant feature transform http://en.wikipedia.org/wiki/Scale-invariant_feature_transform
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module 
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/]  [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) http://www.tsa.gov/what_we_do/layers/twic/index.shtm
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of computer hardware that translates data between parallel and serial interfaces. http://en.wikipedia.org/wiki/UART
# UCB: University of California-Berkeley 
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of 61 academic institutions and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply 
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. http://www.venus.uvic.ca/
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language 
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, www.wmo.ch
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language http://en.wikipedia.org/wiki/XML
# XSD -- XML Schema Definition http://en.wikipedia.org/wiki/XML_Schema
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms.  http://www.act-us.info/
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. www.alfresco.com
# ALOHA-MARS: http://alohamooring.apl.washington.edu/ ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of ~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). http://seahurst.apl.washington.edu/mars.php
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection http://www.mbari.org/aved/
# AWW: All was well. http://www.jkrowling.com/en/
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System http://www.mbari.org/expeditions/Pulse53/gear.htm
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology http://en.wikipedia.org/wiki/Caltech  
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure http://en.wikipedia.org/wiki/Cyberinfrastructure
# CeNCOOS: Central and Northern California Ocean Observing System http://www.cencoos.org/ 
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine http://www.webopedia.com/TERM/C/CNAME.htm 
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison http://www.cs.wisc.edu/condor/
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. http://www.unixgeeks.org/security/newbie/unix/cron-1.html 
# CTD: Conductivity, Temperature, and Depth http://www.whoi.edu/instruments/viewInstrument.do?id=1003
# CVS: Concurrent Versions System; maintains control of history of code/documents 
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. http://en.wikipedia.org/wiki/Demilitarized_zone_(computing) 
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering 
# eGY: the Electronic Geophysical Year http://www.egy.org/
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring.  http://www.mbari.org/mars/general/eits.html
# EOM: Electro-Optical-Mechanical
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network http://www.oceanlab.abdn.ac.uk/research/esonet.php
# ESP: Environmental Sample Processor - Chris Scholin et al. http://www.mbari.org/muse/platforms/ESP.htm
## Darlene was the 1st generation ESP 
## GiGi The first 'second generation' ESP instrument 
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument 
## Bruce Another 'third generation' ESP instrument 
## MOE A third gen. instrument with the MFB connected 
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer 
# GEOSS: Global Earth Observation System of Systems http://www.epa.gov/geoss/
# GUI: Graphical User Interface 
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program 
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces 
# IDE: Integrated Development Environment      
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C++ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See http://www.iode.org/index.php?option=com_content&task=view&id=74 for details.
# IO: Implementing Organization www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf
# IOC: Intergovernmental Oceanographic Commission, http://ioc.unesco.org/iocweb/index.php
# IODE: International Oceanographic Data Exchange, www.iode.org
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, http://ioc.unesco.org/iocweb/index.php
# JIRA: A bug tracking, issue tracking, and project management application http://www.atlassian.com/software/jira/
# JOI: Joint Oceanographic Institutions http://www.joiscience.org/joi
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode 
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap 
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool.  http://maven.apache.org/
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). (http://marinemetadata.org/meta-t )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP 
# MMI: Marine Metadata Initiative http://marinemetadata.org/
# MOBB: Monterey Ocean Bottom Broadband project 
# Modbus: a serial communications protocol http://en.wikipedia.org/wiki/Modbus
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. http://mule.codehaus.org/display/MULE/Home
# MV: Medium Voltage (converter); located in node power supply of MARS 
# Nagios: software to monitor all types of computer and network services. http://www.nagios.org/
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form)             http://www.unidata.ucar.edu/software/netcdf/conventions.html
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. http://www.opengeospatial.org/
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. http://www.ogf.org/
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. http://www.oostethys.org/
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) http://www.pc104.org
# PCA: Principal component analysis. http://en.wikipedia.org/wiki/Principal_components_analysis
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?") 
# pH: a measure of the acidity or alkalinity of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. http://en.wikipedia.org/wiki/PH
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor". 
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives http://en.wikipedia.org/wiki/RAID
# RBI: Runs Batted In
# RC: Radio controlled (airplane) 
# RCO: Regional Cabled Observatory http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems http://www.rosys.com/
# ROV: Remotely Operated Vehicle 
# RS-232 (Recommended Standard 232) is a standard for serial binary data signals connecting between a DTE (Data terminal equipment) and a DCE (Data Circuit-terminating Equipment). It is commonly used in computer serial ports. http://en.wikipedia.org/wiki/RS-232
# RSN: Regional Scale Node. See RCO. http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. (http://www.seadatanet.org/)
# SensorML: not an acronym; markup language to describe sensors and their data. http://vast.uah.edu/SensorML/  
# SIFT: Scale-invariant feature transform http://en.wikipedia.org/wiki/Scale-invariant_feature_transform
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module 
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/]  [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) http://www.tsa.gov/what_we_do/layers/twic/index.shtm
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of computer hardware that translates data between parallel and serial interfaces. http://en.wikipedia.org/wiki/UART
# UCB: University of California-Berkeley 
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of 61 academic institutions and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply 
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. http://www.venus.uvic.ca/
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language 
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, www.wmo.ch
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language http://en.wikipedia.org/wiki/XML
# XSD -- XML Schema Definition http://en.wikipedia.org/wiki/XML_Schema
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms.  http://www.act-us.info/
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. http://www.alfresco.com http://alfresco.mbari.org
# ALOHA-MARS: http://alohamooring.apl.washington.edu/ ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of ~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). http://seahurst.apl.washington.edu/mars.php
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection http://www.mbari.org/aved/
# AWW: All was well. http://www.jkrowling.com/en/
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System http://www.mbari.org/expeditions/Pulse53/gear.htm
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology http://en.wikipedia.org/wiki/Caltech  
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure http://en.wikipedia.org/wiki/Cyberinfrastructure
# CeNCOOS: Central and Northern California Ocean Observing System http://www.cencoos.org/ 
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine http://www.webopedia.com/TERM/C/CNAME.htm 
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison http://www.cs.wisc.edu/condor/
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. http://www.unixgeeks.org/security/newbie/unix/cron-1.html 
# CTD: Conductivity, Temperature, and Depth http://www.whoi.edu/instruments/viewInstrument.do?id=1003
# CVS: Concurrent Versions System; maintains control of history of code/documents 
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. http://en.wikipedia.org/wiki/Demilitarized_zone_(computing) 
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering 
# eGY: the Electronic Geophysical Year http://www.egy.org/
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring.  http://www.mbari.org/mars/general/eits.html
# EOM: Electro-Optical-Mechanical
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network http://www.oceanlab.abdn.ac.uk/research/esonet.php
# ESP: Environmental Sample Processor - Chris Scholin et al. http://www.mbari.org/muse/platforms/ESP.htm
## Darlene was the 1st generation ESP 
## GiGi The first 'second generation' ESP instrument 
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument 
## Bruce Another 'third generation' ESP instrument 
## MOE A third gen. instrument with the MFB connected 
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer 
# GEOSS: Global Earth Observation System of Systems http://www.epa.gov/geoss/
# GUI: Graphical User Interface 
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program 
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces 
# IDE: Integrated Development Environment      
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C++ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See http://www.iode.org/index.php?option=com_content&task=view&id=74 for details.
# IO: Implementing Organization http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf
# IOC: Intergovernmental Oceanographic Commission, http://ioc.unesco.org/iocweb/index.php
# IODE: International Oceanographic Data Exchange, http://www.iode.org
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, http://ioc.unesco.org/iocweb/index.php
# JIRA: A bug tracking, issue tracking, and project management application http://www.atlassian.com/software/jira/
# JOI: Joint Oceanographic Institutions http://www.joiscience.org/joi
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode 
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap 
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool.  http://maven.apache.org/
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). (http://marinemetadata.org/meta-t )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP 
# MMI: Marine Metadata Initiative http://marinemetadata.org/
# MOBB: Monterey Ocean Bottom Broadband project 
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] http://en.wikipedia.org/wiki/Modbus
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. http://mule.codehaus.org/display/MULE/Home
# MV: Medium Voltage (converter); located in node power supply of MARS 
# Nagios: software to monitor all types of computer and network services. http://www.nagios.org/
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form)             http://www.unidata.ucar.edu/software/netcdf/conventions.html
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. http://www.opengeospatial.org/
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. http://www.ogf.org/
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. http://www.oostethys.org/
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) http://www.pc104.org
# PCA: Principal component analysis. http://en.wikipedia.org/wiki/Principal_components_analysis
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?") 
# pH: a measure of the acidity or alkalinity of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. http://en.wikipedia.org/wiki/PH
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor". 
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives http://en.wikipedia.org/wiki/RAID
# RBI: Runs Batted In
# RC: Radio controlled (airplane) 
# RCO: Regional Cabled Observatory http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems http://www.rosys.com/
# ROV: Remotely Operated Vehicle 
# RS-232 (Recommended Standard 232) is a standard for serial binary data signals connecting between a DTE (Data terminal equipment) and a DCE (Data Circuit-terminating Equipment). It is commonly used in computer serial ports. http://en.wikipedia.org/wiki/RS-232
# RSN: Regional Scale Node. See RCO. http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. (http://www.seadatanet.org/)
# SensorML: not an acronym; markup language to describe sensors and their data. http://vast.uah.edu/SensorML/  
# SIFT: Scale-invariant feature transform http://en.wikipedia.org/wiki/Scale-invariant_feature_transform
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module 
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/]  [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) http://www.tsa.gov/what_we_do/layers/twic/index.shtm
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of computer hardware that translates data between parallel and serial interfaces. http://en.wikipedia.org/wiki/UART
# UCB: University of California-Berkeley 
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of 61 academic institutions and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply 
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. http://www.venus.uvic.ca/
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language 
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, www.wmo.ch
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language http://en.wikipedia.org/wiki/XML
# XSD -- XML Schema Definition http://en.wikipedia.org/wiki/XML_Schema
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h3. *Setting up WinCVS (v. 1.2) on your Windows 2000/XP (x86) computer to access the MBARI&nbsp;*{*}{_}moonjelly{_}* *CVS source code repository.*&nbsp;

*1).* To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[http://oceana:8081/display/CLT/CVS+Client+Software+Downloads] and copy&nbsp;the *{_}WinCVS-1.2.0.zip{_}* folder to your Desktop.&nbsp; Extract all files to your *{_}C:\Program_Files{_}*&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
*2).* Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as *{_}C:\Program_Files\GNU\WinCVS_1.2{_}* .

\\
*3).*&nbsp;Once installed, open WinCVS (*{_}Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS{_}*).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says *"ENTER THE CVSROOT"* .&nbsp; An example of this would be (_salamy@moonjelly:/home/cvs_) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the *"AUTHENTIFICATION:"* setting to - *_"passwd" file on the cvs server._*
* Finally, click the _WinCVS_ tab and set your *"home"* directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).
\\

\\
*&nbsp;4).*&nbsp;*NOTE:*&nbsp; To actually use this GUI on the moonjelly repository you will first need an excrypted CVS respository password (see also&nbsp;*"Password Access"* at the following link: [http://oceana:8081/display/CLT/Welcome+to+CVS%21]).
* To do this, telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command {color:#ff0000}{*}{+}encryptCVSpw{+}{*}{color}.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (\*_exactly as listed_\*) to the CVS&nbsp;administrator (*salamy@mbari.org). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.
\\
\\
\\

*5).*&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms.  http://www.act-us.info/
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. http://www.alfresco.com http://alfresco.mbari.org
# ALOHA-MARS: http://alohamooring.apl.washington.edu/ ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of ~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). http://seahurst.apl.washington.edu/mars.php
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection http://www.mbari.org/aved/
# AWW: All was well. http://www.jkrowling.com/en/
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System http://www.mbari.org/expeditions/Pulse53/gear.htm
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology http://en.wikipedia.org/wiki/Caltech  
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure http://en.wikipedia.org/wiki/Cyberinfrastructure
# CeNCOOS: Central and Northern California Ocean Observing System http://www.cencoos.org/ 
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine http://www.webopedia.com/TERM/C/CNAME.htm 
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison http://www.cs.wisc.edu/condor/
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. http://www.unixgeeks.org/security/newbie/unix/cron-1.html 
# CTD: Conductivity, Temperature, and Depth http://www.whoi.edu/instruments/viewInstrument.do?id=1003
# CVS: Concurrent Versions System; maintains control of history of code/documents 
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. http://en.wikipedia.org/wiki/Demilitarized_zone_(computing) 
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering 
# eGY: the Electronic Geophysical Year http://www.egy.org/
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring.  http://www.mbari.org/mars/general/eits.html
# EOM: Electro-Optical-Mechanical
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network http://www.oceanlab.abdn.ac.uk/research/esonet.php
# ESP: Environmental Sample Processor - Chris Scholin et al. http://www.mbari.org/muse/platforms/ESP.htm
## Darlene was the 1st generation ESP 
## GiGi The first 'second generation' ESP instrument 
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument 
## Bruce Another 'third generation' ESP instrument 
## MOE A third gen. instrument with the MFB connected 
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer 
# GEOSS: Global Earth Observation System of Systems http://www.epa.gov/geoss/
# GUI: Graphical User Interface 
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program 
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces 
# IDE: Integrated Development Environment      
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C++ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See http://www.iode.org/index.php?option=com_content&task=view&id=74 for details.
# IO: Implementing Organization http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf
# IOC: Intergovernmental Oceanographic Commission, http://ioc.unesco.org/iocweb/index.php
# IODE: International Oceanographic Data Exchange, http://www.iode.org
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, http://ioc.unesco.org/iocweb/index.php
# JIRA: A bug tracking, issue tracking, and project management application http://www.atlassian.com/software/jira/
# JOI: Joint Oceanographic Institutions http://www.joiscience.org/joi
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode 
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap 
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool.  http://maven.apache.org/
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). (http://marinemetadata.org/meta-t )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP 
# MMI: Marine Metadata Initiative http://marinemetadata.org/
# MOBB: Monterey Ocean Bottom Broadband project 
# Modbus: a serial communications protocol http://en.wikipedia.org/wiki/Modbus
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. http://mule.codehaus.org/display/MULE/Home
# MV: Medium Voltage (converter); located in node power supply of MARS 
# Nagios: software to monitor all types of computer and network services. http://www.nagios.org/
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form)             http://www.unidata.ucar.edu/software/netcdf/conventions.html
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. http://www.opengeospatial.org/
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. http://www.ogf.org/
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. http://www.oostethys.org/
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) http://www.pc104.org
# PCA: Principal component analysis. http://en.wikipedia.org/wiki/Principal_components_analysis
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?") 
# pH: a measure of the acidity or alkalinity of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. http://en.wikipedia.org/wiki/PH
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor". 
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives http://en.wikipedia.org/wiki/RAID
# RBI: Runs Batted In
# RC: Radio controlled (airplane) 
# RCO: Regional Cabled Observatory http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems http://www.rosys.com/
# ROV: Remotely Operated Vehicle 
# RS-232 (Recommended Standard 232) is a standard for serial binary data signals connecting between a DTE (Data terminal equipment) and a DCE (Data Circuit-terminating Equipment). It is commonly used in computer serial ports. http://en.wikipedia.org/wiki/RS-232
# RSN: Regional Scale Node. See RCO. http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. (http://www.seadatanet.org/)
# SensorML: not an acronym; markup language to describe sensors and their data. http://vast.uah.edu/SensorML/  
# SIFT: Scale-invariant feature transform http://en.wikipedia.org/wiki/Scale-invariant_feature_transform
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module 
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/]  [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) http://www.tsa.gov/what_we_do/layers/twic/index.shtm
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of computer hardware that translates data between parallel and serial interfaces. http://en.wikipedia.org/wiki/UART
# UCB: University of California-Berkeley 
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of 61 academic institutions and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply 
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. http://www.venus.uvic.ca/
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language 
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, www.wmo.ch
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language http://en.wikipedia.org/wiki/XML
# XSD -- XML Schema Definition http://en.wikipedia.org/wiki/XML_Schema
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools

h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed. 

See [Maven At MBARI] for more details.

h3. Modelling with UML (Together)

After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

{warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN{code}{warning}

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.]]></property>
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# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - http://ican.science.oregonstate.edu/home
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://confluence.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts an externally accessable Maven repository at [https://oceana.mbari.org/maven2], an internal repository at [http://seaspray.shore.mbari.org:8082/archiva/repository/internal/] and a repository manager at [http://seaspray.shore.mbari.org:8082/archiva]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modeling with UML (JBuilder 2008 Enterprise)

You can download JBuilder 2008 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded and installed, you need to copy the following [.slip|https://alfresco.mbari.org/alfresco/webdav/Engineering/Tools/Collaboration%20Tools/CodeGear%20JBuilder/concurrent_31474.slip] file to the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">11239958</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">15663630</id>
<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOI CI: Ocean Observatories Initiative CyberInfrastructure: http://ci.oceanobservatories.org/&nbsp; (Developers site: http://ooici.net/)
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software Integration).&nbsp;
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">15630876</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">15663628</id>
<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software Integration).&nbsp;
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts an externally accessable Maven repository at [https://oceana.mbari.org/maven2], an internal repository at [http://seaspray.shore.mbari.org:8082/archiva/repository/internal/] and a repository manager at [http://seaspray.shore.mbari.org:8082/archiva]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modeling with UML (JBuilder 2008 Enterprise)

You can download JBuilder 2008 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded and installed, you need to copy the following [.slip|https://alfresco.mbari.org/alfresco/webdav/Engineering/Tools/Collaboration%20Tools/CodeGear%20JBuilder/concurrent_31474.slip] file to the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ARI-WG: Access to Remote Instrumentation in a distributed environment - Working Group. OpenGrid Forum [http://www.ogf.org/gf/group_info/view.php?group=ari-wg]
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MB/CA Current: a MBARI project in 2011
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOI CI: Ocean Observatories Initiative CyberInfrastructure: [http://ci.oceanobservatories.org/] (Developers site: [http://ooici.net/])
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software).
# SCPI: Self Contained Plankton Imager, an MBARI project in 2011
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[h3. Introduction
This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h3. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h4. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select 
More Actions/View Details, then "Create Shortcut" (on the right side fo the page). 

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h4. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h4. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h4. Modelling with UML (Together)

After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:

# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.  

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There are&nbsp;two recommended CVS Clients to access the MBARI CVS Respository including:&nbsp;{color:#ff0000}{*}WinCVS{*}{color} and {color:#ff0000}{*}SmartCVS{*}{color}.&nbsp;&nbsp; Both clients work for all major operating systems including Windows, Macintosh, and Linux systems.&nbsp;The key bits of information to use when setting up either client are the following:
* {color:#0000cc}Your access method needs to be set to&nbsp;{color}{color:#0000cc}{*}pserver{*}{color}{color:#0000cc}&nbsp;(SmartCVS) or{color} {color:#0000cc}{*}passwd file on server{*}{color} {color:#0000cc}(WinCVS){color}
* {color:#0000cc}User&nbsp; (Your MBARI user/e-mail&nbsp;account, e.g.,{color} {color:#0000cc}{_}salamy{_}{color}{color:#0000cc}){color}
* {color:#0000cc}Repository Server (MBARI CVS Repository is hosted on{color} {color:#0000cc}{*}{_}moonjelly.shore.mbari.org{_}{*}{color}{color:#0000cc}){color}
* {color:#0000cc}CVSROOT ({color}{color:#0000cc}{*}_/home/cvs{_}{*}{color}{color:#0000cc}){color}

Thus, the full CVSROOT path for user _salamy_ would be:&nbsp;&nbsp;&nbsp; salamy@moonjelly.shore.mbari.org:/home/cvs&nbsp;

----
\\

h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Windows-7.1.3.zip|^smartcvs-win32-setup-nojre-7_1_3.zip|SmartCVS Windows version 7.1.3] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOSX-7.1.3.tar.gz|^smartcvs-macosx-7_1_3.tar.gz|SmartCVS Macintosh Version 7.1.3] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartSVN-Linux-7.1.3.tar.gz|^smartcvs-generic-7_1_3.tar.gz|SmartSVN Linux Version 7.1.3] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}({color}{color:#0066cc}{*}NOTE:*{color}{color:#0066cc}&nbsp;Setup same for MacCVS and gCVS as well){color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS Getting-Started Tutorial|^smartcvs-tutorial.pdf] \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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h3. *Setting up WinCVS (v. 1.2) on your Windows 2000/XP (x86) computer to access the MBARI&nbsp;*{*}{_}moonjelly{_}* *CVS source code repository.*&nbsp;

*1).* To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[http://oceana:8081/display/CLT/CVS+Client+Software+Downloads] and copy&nbsp;the *{_}WinCVS-1.2.0.zip{_}* folder to your Desktop.&nbsp; Extract all files to your *{_}C:\Program_Files{_}*&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
*2).* Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as *{_}C:\Program_Files\GNU\WinCVS_1.2{_}* .

\\
*3).*&nbsp;Once installed, open WinCVS (*{_}Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS{_}*).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says *"ENTER THE CVSROOT"* .&nbsp; An example of this would be (_salamy@moonjelly:/home/cvs_) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the *"AUTHENTIFICATION:"* setting to - *_"passwd" file on the cvs server._*
* Finally, click the _WinCVS_ tab and set your *"home"* directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).
\\

\\
*&nbsp;4).*&nbsp;*NOTE:*&nbsp; To actually use this GUI on the moonjelly repository you will first need an excrypted CVS respository password (see also&nbsp;*"Password Access"* at the following link: [http://oceana:8081/display/CLT/Welcome+to+CVS%21]).
* To do this, telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command&nbsp;*"*{color:#ff0000}{*}encryptCVSpw{*}{color}{color:#000000}*"*{color}*.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (*{_}exactly as listed{_}*) to the CVS&nbsp;administrator (*salamy@mbari.org*). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.
\\
\\
\\

*5).*&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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h3. *Setting up WinCVS (v. 1.2) on your Windows 2000/XP (x86) computer to access the MBARI&nbsp;*{*}{_}moonjelly{_}* *CVS source code repository.*&nbsp;

*1).* To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[http://oceana:8081/display/CLT/CVS+Client+Software+Downloads] and copy&nbsp;the *{_}WinCVS-1.2.0.zip{_}* folder to your Desktop.&nbsp; Extract all files to your *{_}C:\Program_Files{_}*&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
*2).* Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as *{_}C:\Program_Files\GNU\WinCVS_1.2{_}* .

\\
*3).*&nbsp;Once installed, open WinCVS (*{_}Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS{_}*).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says *"ENTER THE CVSROOT"* .&nbsp; An example of this would be (_salamy@moonjelly:/home/cvs_) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the *"AUTHENTIFICATION:"* setting to - *_"passwd" file on the cvs server._*
* Finally, click the _WinCVS_ tab and set your *"home"* directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).
\\

\\
*&nbsp;4).*&nbsp;*NOTE:*&nbsp; To actually use this GUI on the moonjelly repository you will first need an excrypted CVS respository password (see also&nbsp;*"Password Access"* at the following link: [http://oceana:8081/display/CLT/Welcome+to+CVS%21]).
* To do this, telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command&nbsp;*"*{color:#ff0000}{*}encryptCVSpw{*}{color}{color:#000000}*"*{color}.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (*{_}exactly as listed{_}*) to the CVS&nbsp;administrator (*salamy@mbari.org*). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.
\\
\\
\\

*5).*&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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h3. *Setting up WinCVS (v. 1.2) on your Windows 2000/XP (x86) computer to access the MBARI&nbsp;*{*}{_}moonjelly{_}* *CVS source code repository.*&nbsp;

*1).* To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[http://oceana:8081/display/CLT/CVS+Client+Software+Downloads] and copy&nbsp;the *{_}WinCVS-1.2.0.zip{_}* folder to your Desktop.&nbsp; Extract all files to your *{_}C:\Program_Files{_}*&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
*2).* Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as *{_}C:\Program_Files\GNU\WinCVS_1.2{_}* .

\\
*3).*&nbsp;Once installed, open WinCVS (*{_}Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS{_}*).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says *"ENTER THE CVSROOT"* .&nbsp; An example of this would be (_salamy@moonjelly:/home/cvs_) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the *"AUTHENTIFICATION:"* setting to - *_"passwd" file on the cvs server._*
* Finally, click the _WinCVS_ tab and set your *"home"* directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).
\\

\\
*&nbsp;4).*&nbsp;*NOTE:*&nbsp; To actually use this GUI on the moonjelly repository you will first need an excrypted CVS respository password (see also&nbsp;*"Password Access"* at the following link: [http://oceana:8081/display/CLT/Welcome+to+CVS%21]).
* To do this, telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command&nbsp; *"encryptCVSpw"*&nbsp;*.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (*{_}exactly as listed{_}*) to the CVS&nbsp;administrator (*salamy@mbari.org). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.
\\
\\
\\

*5).*&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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<property name="body"><![CDATA[----
h3. *Setting up WinCVS (v. 1.2) on your Windows 2000/XP (x86) computer to access the MBARI&nbsp;*{*}{_}moonjelly{_}* *CVS source code repository.*&nbsp;

*1).* To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[http://oceana:8081/display/CLT/CVS+Client+Software+Downloads] and copy&nbsp;the *{_}WinCVS-1.2.0.zip{_}* folder to your Desktop.&nbsp; Extract all files to your *{_}C:\Program_Files{_}*&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
*2).* Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as *{_}C:\Program_Files\GNU\WinCVS_1.2{_}* .

\\
*3).*&nbsp;Once installed, open WinCVS (*{_}Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS{_}*).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says *"ENTER THE CVSROOT"* .&nbsp; An example of this would be (_salamy@moonjelly:/home/cvs_) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the *"AUTHENTIFICATION:"* setting to - *_"passwd" file on the cvs server._*
* Finally, click the _WinCVS_ tab and set your *"home"* directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).
\\

\\
*&nbsp;4).*&nbsp;*NOTE:*&nbsp; To actually use this GUI on the moonjelly repository you will first need an excrypted CVS respository password (see also&nbsp;*"Password Access"* at the following link: [http://oceana:8081/display/CLT/Welcome+to+CVS%21]).
* To do this, telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command&nbsp; *"*{color:#ff0000}{*}encryptCVSpw{*}{color}*"*&nbsp;*.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (*{_}exactly as listed_\*) to the CVS&nbsp;administrator (*salamy@mbari.org). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.
\\
\\
\\

*5).*&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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h3. *Setting up WinCVS (v. 1.2) on your Windows 2000/XP (x86) computer to access the MBARI&nbsp;*{*}{_}moonjelly{_}* *CVS source code repository.*&nbsp;

*1).* To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[http://oceana:8081/display/CLT/CVS+Client+Software+Downloads] and copy&nbsp;the *{_}WinCVS-1.2.0.zip{_}* folder to your Desktop.&nbsp; Extract all files to your *{_}C:\Program_Files{_}*&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
*2).* Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as *{_}C:\Program_Files\GNU\WinCVS_1.2{_}* .

\\
*3).*&nbsp;Once installed, open WinCVS (*{_}Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS{_}*).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says *"ENTER THE CVSROOT"* .&nbsp; An example of this would be (_salamy@moonjelly:/home/cvs_) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the *"AUTHENTIFICATION:"* setting to - *_"passwd" file on the cvs server._*
* Finally, click the _WinCVS_ tab and set your *"home"* directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).
\\

\\
*&nbsp;4).*&nbsp;*NOTE:*&nbsp; To actually use this GUI on the moonjelly repository you will first need an excrypted CVS respository password (see also&nbsp;*"Password Access"* at the following link: [http://oceana:8081/display/CLT/Welcome+to+CVS%21]).
* To do this, telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command *"*{color:#ff0000}{*}encryptCVSpw{*}{color}*"*"*&nbsp;*.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (\*_exactly as listed_\*) to the CVS&nbsp;administrator (*salamy@mbari.org). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.
\\
\\
\\

*5).*&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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<property name="body"><![CDATA[----
h3. *Setting up WinCVS (v. 1.2) on your Windows 98/NT/2000 (x86) computer to access the moonjelly CVS source code repository.*&nbsp;

*1).* To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[http://oceana:8081/display/CLT/CVS+Client+Software+Downloads] and copy&nbsp;the WinCVS-1.2.0.zip zip folder to your Desktop.&nbsp; Extract all files to your C:\Program_Files&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
*2).* Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as C:\Program_Files\GNU\WinCVS_1.2 .

\\
*3).*&nbsp;Once installed, open WinCVS (Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says "ENTER THE CVSROOT" .&nbsp; An example of this would be (salamy@moonjelly:/home/cvs) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the "AUTHENTIFICATION:" setting to - *_"passwd" file on the cvs server{_}*
* Finally, click the _WinCVS_ tab and set your "home" directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.). \\

\\
*&nbsp;4).*&nbsp;*NOTE:*&nbsp; To actually use this GUI on the moonjelly repository you will first need an excrypted CVS respository password (see also&nbsp;*"Password Access"* at the following link: [http://oceana:8081/display/CLT/Welcome+to+CVS%21]).
* To do this, telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command&nbsp;*"{color:#ff0000}{*}encryptCVSpw{*}{color}"*.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (*{_}exactly as listed{_}*) to the CVS&nbsp;administrator (*salamy@mbari.org*). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
*NOTE:*&nbsp; A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.
\\ \\

*5).*&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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h3. *Setting up WinCVS (v. 1.2) on your Windows 2000/XP (x86) computer to access the MBARI&nbsp;*{*}{_}moonjelly{_}* *CVS source code repository.*&nbsp;

*1).* To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[http://oceana:8081/display/CLT/CVS+Client+Software+Downloads] and copy&nbsp;the *{_}WinCVS-1.2.0.zip{_}* folder to your Desktop.&nbsp; Extract all files to your *{_}C:\Program_Files{_}*&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
*2).* Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as *{_}C:\Program_Files\GNU\WinCVS_1.2{_}* .

\\
*3).*&nbsp;Once installed, open WinCVS (_Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS_).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says *"ENTER THE CVSROOT"* .&nbsp; An example of this would be (_salamy@moonjelly:/home/cvs_) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the *"AUTHENTIFICATION:"* setting to - *_"passwd" file on the cvs server._*
* Finally, click the _WinCVS_ tab and set your *"home"* directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).
\\

\\
*&nbsp;4).*&nbsp;*NOTE:*&nbsp; To actually use this GUI on the moonjelly repository you will first need an excrypted CVS respository password (see also&nbsp;*"Password Access"* at the following link: [http://oceana:8081/display/CLT/Welcome+to+CVS%21]).
* To do this, telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command&nbsp;*"*{color:#ff0000}{*}encryptCVSpw{*}{color}*"*.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (*{_}exactly as listed{_}*) to the CVS&nbsp;administrator (*salamy@mbari.org*). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.
\\
\\

*5).*&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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h3. *Setting up WinCVS (v. 1.2) on your Windows 2000/XP (x86) computer to access the MBARI&nbsp;*{*}{_}moonjelly{_}* *CVS source code repository.*&nbsp;

*1).* To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[http://oceana:8081/display/CLT/CVS+Client+Software+Downloads] and copy&nbsp;the *{_}WinCVS-1.2.0.zip{_}* folder to your Desktop.&nbsp; Extract all files to your *{_}C:\Program_Files{_}*&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
*2).* Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as *{_}C:\Program_Files\GNU\WinCVS_1.2{_}* .

\\
*3).*&nbsp;Once installed, open WinCVS (_Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS_).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says *"ENTER THE CVSROOT"* .&nbsp; An example of this would be (_salamy@moonjelly:/home/cvs_) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the *"AUTHENTIFICATION:"* setting to - *_"passwd" file on the cvs server._*
* Finally, click the _WinCVS_ tab and set your *"home"* directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).
\\

\\
*&nbsp;4).*&nbsp;*NOTE:*&nbsp; To actually use this GUI on the moonjelly repository you will first need an excrypted CVS respository password (see also&nbsp;*"Password Access"* at the following link: [http://oceana:8081/display/CLT/Welcome+to+CVS%21]).
* To do this, telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command&nbsp;*"{color:#ff0000}{*}encryptCVSpw{*}{color}"*.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (*{_}exactly as listed{_}*) to the CVS&nbsp;administrator (*salamy@mbari.org*). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.
\\
\\ \\

*5).*&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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h3. *Setting up WinCVS (v. 1.2) on your Windows 2000/XP (x86) computer to access the MBARI&nbsp;*{*}{_}moonjelly{_}* *CVS source code repository.*&nbsp;

*1).* To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[http://oceana:8081/display/CLT/CVS+Client+Software+Downloads] and copy&nbsp;the *{_}WinCVS-1.2.0.zip{_}* folder to your Desktop.&nbsp; Extract all files to your *{_}C:\Program_Files{_}*&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
*2).* Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as *{_}C:\Program_Files\GNU\WinCVS_1.2{_}* .

\\
*3).*&nbsp;Once installed, open WinCVS (*{_}Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS{_}*).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says *"ENTER THE CVSROOT"* .&nbsp; An example of this would be (_salamy@moonjelly:/home/cvs_) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the *"AUTHENTIFICATION:"* setting to - *_"passwd" file on the cvs server._*
* Finally, click the _WinCVS_ tab and set your *"home"* directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).
\\

\\
*&nbsp;4).*&nbsp;*NOTE:*&nbsp; To actually use this GUI on the moonjelly repository you will first need an excrypted CVS respository password (see also&nbsp;*"Password Access"* at the following link: [http://oceana:8081/display/CLT/Welcome+to+CVS%21]).
* To do this, telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command&nbsp;*"*{color:#ff0000}{*}encryptCVSpw{*}{color}*"*.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (*{_}exactly as listed{_}*) to the CVS&nbsp;administrator (*salamy@mbari.org*). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.
\\
\\
\\

*5).*&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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h3. *Setting up WinCVS (v. 1.2) on your Windows 2000/XP (x86) computer to access the MBARI&nbsp;*{*}{_}moonjelly{_}* *CVS source code repository.*&nbsp;

*1).* To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[http://oceana:8081/display/CLT/CVS+Client+Software+Downloads] and copy&nbsp;the *{_}WinCVS-1.2.0.zip{_}* folder to your Desktop.&nbsp; Extract all files to your *{_}C:\Program_Files{_}*&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
*2).* Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as *{_}C:\Program_Files\GNU\WinCVS_1.2{_}* .

\\
*3).*&nbsp;Once installed, open WinCVS (*{_}Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS{_}*).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says *"ENTER THE CVSROOT"* .&nbsp; An example of this would be (_salamy@moonjelly:/home/cvs_) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the *"AUTHENTIFICATION:"* setting to - *_"passwd" file on the cvs server._*
* Finally, click the _WinCVS_ tab and set your *"home"* directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).
\\

\\
*&nbsp;4).*&nbsp;*NOTE:*&nbsp; To actually use this GUI on the moonjelly repository you will first need an excrypted CVS respository password (see also&nbsp;*"Password Access"* at the following link: [http://oceana:8081/display/CLT/Welcome+to+CVS%21]).
* To do this, telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command&nbsp;*"*{color:#ff0000}{*}encryptCVSpw{*}{color}{color:#000000}*"*{color}*.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (*{_}exactly as listed{_}*) to the CVS&nbsp;administrator (*salamy@mbari.org*). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.
\\
\\
\\

*5).*&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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h3. *Setting up WinCVS (v. 1.2) on your Windows 2000/XP (x86) computer to access the MBARI&nbsp;*{*}{_}moonjelly{_}* *CVS source code repository.*&nbsp;

*1).* To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[http://oceana:8081/display/CLT/CVS+Client+Software+Downloads] and copy&nbsp;the *{_}WinCVS-1.2.0.zip{_}* folder to your Desktop.&nbsp; Extract all files to your *{_}C:\Program_Files{_}*&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
*2).* Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as *{_}C:\Program_Files\GNU\WinCVS_1.2{_}* .

\\
*3).*&nbsp;Once installed, open WinCVS (*{_}Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS{_}*).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says *"ENTER THE CVSROOT"* .&nbsp; An example of this would be (_salamy@moonjelly:/home/cvs_) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the *"AUTHENTIFICATION:"* setting to - *_"passwd" file on the cvs server._*
* Finally, click the _WinCVS_ tab and set your *"home"* directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).
\\

\\
*&nbsp;4).*&nbsp;*NOTE:*&nbsp; To actually use this GUI on the moonjelly repository you will first need an excrypted CVS respository password (see also&nbsp;*"Password Access"* at the following link: [http://oceana:8081/display/CLT/Welcome+to+CVS%21]).
* To do this, telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command&nbsp;*"*{color:#ff0000}{*}encryptCVSpw{*}{color}{color:#000000}*"*{color}.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (*{_}exactly as listed{_}*) to the CVS&nbsp;administrator (*salamy@mbari.org*). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.
\\
\\
\\

*5).*&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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----
*[*Welcome to CVS\!*|http://oceana:8081/display/CLT/Welcome+to+CVS%21]*

*[*Setting up a CVS Graphical User Interface (GUI)*|CLT:CVS Client Software Downloads^Setting up WinCVS_1.2_new.doc]*

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator (_Karen Salamy:&nbsp;_ salamy@mbari.org). Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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<property name="body"><![CDATA[----
h3. *Setting up WinCVS (v. 1.2) on your Windows 98/NT/2000 (x86) computer to access the moonjelly CVS source code repository.*&nbsp;

*1).* To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[http://oceana:8081/display/CLT/CVS+Client+Software+Downloads] and copy&nbsp;the WinCVS-1.2.0.zip zip folder to your Desktop.&nbsp; Extract all files to your C:\Program_Files&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
*2).* Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as C:\Program_Files\GNU\WinCVS_1.2 .

\\
*3).*&nbsp;Once installed, open WinCVS (Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says "ENTER THE CVSROOT" .&nbsp; An example of this would be (salamy@moonjelly:/home/cvs) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the "AUTHENTIFICATION:" setting to - *_"passwd" file on the cvs server{_}*
* Finally, click the _WinCVS_ tab and set your "home" directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).
\\

*&nbsp;4).*&nbsp; *NOTE:*&nbsp; To actually use this GUI on the moonjelly repository you will first need an excrypted CVS respository password (see also&nbsp;*"Password Access"* at the following link: http://oceana:8081/display/CLT/Welcome+to+CVS%21).
* To do this, telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command&nbsp;*"*{color:#ff0000}{*}encryptCVSpw{*}{color}*"*.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (*{_}exactly as listed{_}*) to the CVS&nbsp;administrator (*salamy@mbari.org*). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
*NOTE:*&nbsp; A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.
\\

&nbsp;*5).*&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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<property name="body"><![CDATA[----
h3. *Setting up WinCVS (v. 1.2) on your Windows 98/NT/2000 (x86) computer to access the moonjelly CVS source code repository.*&nbsp;

*1).* To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[http://oceana:8081/display/CLT/CVS+Client+Software+Downloads] and copy&nbsp;the WinCVS-1.2.0.zip zip folder to your Desktop.&nbsp; Extract all files to your C:\Program_Files&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
*2).* Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as C:\Program_Files\GNU\WinCVS_1.2 .

\\
*3).*&nbsp;Once installed, open WinCVS (Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says "ENTER THE CVSROOT" .&nbsp; An example of this would be (salamy@moonjelly:/home/cvs) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the "AUTHENTIFICATION:" setting to - *_"passwd" file on the cvs server{_}*
* Finally, click the _WinCVS_ tab and set your "home" directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).
\\

*&nbsp;4).*&nbsp; *PLEASE NOTE:* To actually use this GUI on the moonjelly repository you will first need:
* An encrypted CVS repository password. Telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command&nbsp;*"{color:#ff0000}{*}encryptCVSpw{*}{color}"*.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (*{_}exactly as listed{_}*) to the CVS&nbsp;administrator (*salamy@mbari.org*). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
*NOTE:*&nbsp; A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.\\

&nbsp;*5).*&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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{gliffy:name=Secure SVN Operational Diagram|space=CLT|page=Secure SVN Development|pageid=9372190|align=left|size=L}]]></property>
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<property name="body"><![CDATA[----
h3. *Setting up WinCVS (v. 1.2) on your Windows 98/NT/2000 (x86) computer to access the moonjelly CVS source code repository.*&nbsp;

1). To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[http://oceana:8081/display/CLT/CVS+Client+Software+Downloads] and copy&nbsp;the WinCVS-1.2.0.zip zip folder to your Desktop.&nbsp; Extract all files to your C:\Program_Files&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
2). Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as C:\Program_Files\GNU\WinCVS_1.2
\\

3).&nbsp;Once installed, open WinCVS (Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS).
The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says "ENTER THE CVSROOT" .&nbsp; An example of this would be (salamy@moonjelly:/home/cvs) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the "AUTHENTIFICATION:" setting to - *_"passwd" file on the cvs server{_}*
* Finally, click the _WinCVS_ tab and set your "home" directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).\\

&nbsp;&nbsp;4).&nbsp; *PLEASE NOTE:* To actually use this GUI on the moonjelly repository you will first need:
* An encrypted CVS repository password. Telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command&nbsp;*"*{color:#ff0000}{*}encryptCVSpw{*}{color}*"*.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (*{_}exactly as listed{_}*) to the CVS&nbsp;administrator (*salamy@mbari.org*). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to access the&nbsp;repository.
&nbsp;
*NOTE:*&nbsp; A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if&nbsp;you know exactly where the files are to be stored or retrieved.


&nbsp;&nbsp;5).&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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h3. *Setting up WinCVS (v. 1.2) on your Windows 98/NT/2000 (x86) computer to access the moonjelly CVS source code repository.*&nbsp;

1). To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[http://oceana:8081/display/CLT/CVS+Client+Software+Downloads] and copy&nbsp;the WinCVS-1.2.0.zip zip folder to your Desktop.&nbsp; Extract all files to your C:\Program_Files&nbsp;folder for installation.&nbsp;

&nbsp;&nbsp;
2). Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as C:\Program_Files\GNU\WinCVS_1.2
\\

3).&nbsp;Once installed, open WinCVS (Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS).
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says "ENTER THE CVSROOT" .&nbsp; An example of this would be (salamy@moonjelly:/home/cvs) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the "AUTHENTIFICATION:" setting to - *_"passwd" file on the cvs server{_}*
* Finally, click the _WinCVS_ tab and set your "home" directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).

&nbsp;&nbsp;4).&nbsp; *PLEASE NOTE:* To actually use this GUI on the moonjelly repository you will first need:
&nbsp;
\-&nbsp;&nbsp;&nbsp;&nbsp; An encrypted CVS repository password. Telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command&nbsp;*"{color:#ff0000}{*}encryptCVSpw{*}{color}"*.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (*{_}exactly as listed{_}*) to the CVS&nbsp;administrator (*salamy@mbari.org*). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; access the&nbsp;repository.
&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *NOTE:*&nbsp; A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; you know exactly where the files are to be stored or retrieved.
&nbsp;&nbsp;5).&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*\**\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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<property name="body"><![CDATA[----
h3. *Setting up WinCVS (v. 1.2) on your Windows 98/NT/2000 (x86) computer to access the moonjelly CVS source code repository.*&nbsp;

1). To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;[http://oceana:8081/display/CLT/CVS+Client+Software+Downloads] and copy&nbsp;the WinCVS-1.2.0.zip zip folder to your Desktop.&nbsp; Extract all files to your C:\Program_Files&nbsp;folder for installation.&nbsp;


&nbsp;&nbsp;
2). Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as C:\Program_Files\GNU\WinCVS_1.2\\


3).&nbsp;Once installed, open WinCVS (Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS).
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
* Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says "ENTER THE CVSROOT" .&nbsp; An example of this would be (salamy@moonjelly:/home/cvs) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
* Still under the _General_ tab, set the "AUTHENTIFICATION:" setting to - *_"passwd" file on the cvs server{_}** Finally, click the _WinCVS_ tab and set your "home" directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).


&nbsp;&nbsp;4).&nbsp; *PLEASE NOTE:* To actually use this GUI on the moonjelly repository you will first need:
&nbsp;
\-&nbsp;&nbsp;&nbsp;&nbsp; An encrypted CVS repository password. Telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command&nbsp;*"*{color:#ff0000}{*}encryptCVSpw{*}{color}*"*.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (*{_}exactly as listed{_}*) to the CVS&nbsp;administrator (*salamy@mbari.org*). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; access the&nbsp;repository.
&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *NOTE:*&nbsp; A good way to maneuver through the repository with your GUI is to have your web browser open to: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at] the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; you know exactly where the files are to be stored or retrieved.
&nbsp;&nbsp;5).&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \***\**CVS exited normally with code 0*\****.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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<property name="body"><![CDATA[{gliffy:name=Secure SVN Operational Diagram|space=CLT|page=Secure SVN Development|pageid=9372190|align=left|size=L}

h5. Desired behavior
# We can create accounts on Subversion (Crowd local store is where we can do this) for external collaborators.  This will prevent them from having any access to  MBARI resources.
# It may eventually get to the point where users can create new repositories (projects), but for now, we will assume that the 

h5. References
# [Integrating Crowd with Apache|http://confluence.atlassian.com/display/CROWD/Integrating+Crowd+with+Apache]
# [Integrating Crowd with Subversion|http://confluence.atlassian.com/display/CROWD/Integrating+Crowd+with+Subversion]]]></property>
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<property name="body"><![CDATA[----
*I.**&nbsp;* *Setting up WinCVS (v. 1.2) on your Windows 98/NT/2000 (x86) computer to access the moonjelly CVS source code repository.* 
1). To install WinCVS 1.2 on your computer please go to:&nbsp;&nbsp;http://oceana:8081/display/CLT/CVS+Client+Software+Downloads and copy&nbsp;the WinCVS-1.2.0.zip zip folder to your Desktop.&nbsp; Extract all files to your C:\Program_Files&nbsp;folder for installation.&nbsp;
&nbsp; 
2). Next, open the WinCVS120 folder and double click on the {color:#ff0000}{*}Setup.exe{*}{color} icon.&nbsp; WinCVS&nbsp;should install on your computers' harddrive as C:\Program_Files\GNU\WinCVS_1.2
&nbsp; 3).&nbsp;Once installed, open WinCVS (Startmenu - Programs - GNU - WinCVS_1.2 - WinCVS).
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The following edits will need to be performed for the GUI to "view" the moonjelly CVS&nbsp;repository.
 \-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Under *Admin* on the main menu - click *Preferences*.&nbsp; Under the _General_ tab enter your ID name and repository information where it says "ENTER THE CVSROOT" .&nbsp; An example of this would be (salamy@moonjelly:/home/cvs) .&nbsp; Users would type this in exactly, replacing only their ID names for "salamy".&nbsp; This sets the path to the moonjelly repository (/home/cvs) and logs in the user.&nbsp; *NOTE:*&nbsp; Your ID name is your e-mail name (the part before the @mbari.org).
 \-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Still under the _General_ tab, set the "AUTHENTIFICATION:" setting to - *_"passwd" file on the cvs server{_}*
 
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Finally, click the _WinCVS_ tab and set your "home" directory (aka. working directory or sandbox).&nbsp; This directory is where you will download repository files to make edits or add files.&nbsp; It is suggested to place this directory on the MBARI network (e.g., Tornado, Tempest) where it will be backed up nightly.&nbsp; Also, indicate the editor that you would like to view repository files with (e.g., CodeWarrior, emacs, etc.).
&nbsp; 4).&nbsp; *PLEASE NOTE:* To actually use this GUI on the moonjelly repository you will first need:
 
\-&nbsp;&nbsp;&nbsp;&nbsp; An encrypted CVS repository password. Telnet to moonjelly with your MBARI UNIX&nbsp;account (NIS password) and at the initial prompt type the command&nbsp;*"*{color:#ff0000}{*}encryptCVSpw{*}{color}*"*.&nbsp; This runs a script requesting you to create and verify a password&nbsp;for the CVS repository.&nbsp; It outputs an&nbsp;&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; encrypted version of that password.&nbsp; Please&nbsp;copy and e-mail the ENCRYPTED password (exactly as listed) to the CVS&nbsp;administrator (salamy@mbari.org). You will receive an e-mail verification stating that&nbsp;the password account has been updated.&nbsp; You should then be able to &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; access the&nbsp;repository.
 
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *NOTE:*&nbsp; A good way to maneuver through the repository with your GUI is to have your web browser open to: http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/&nbsp;at the same time in order to "view" the module's directory structure.&nbsp; This will greatly simplify your use of the system if

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; you know exactly where the files are to be stored or retrieved.
&nbsp; 5).&nbsp; Next, click *Admin* on main menu - click *Login*.&nbsp; Type in your requested repository password&nbsp;(normal text - not the scripts' encrypted text\!).&nbsp; If you were able to log in properly you should&nbsp;see a line that says \*****CVS exited normally with code 0****\*.&nbsp; Odd as it seems, this is
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; correct. ]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools

h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed. 

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool.  It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant.  You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory.

{note:Together has been Deprecated}
We have moved to JBuilder 2007 (see notes above).
{note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

{warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN{code}{warning}

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.]]></property>
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<property name="body"><![CDATA[----
h3. *{+}Welcome to CVS\!+*

CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp;&nbsp;Someone has&nbsp;requested that you be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

h3. \\


h3. +Permissions+

Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. _moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot access _moonjelly_ for any reason, please let me know.

\\
&nbsp;

h3. +Password Access+

Access to the repository requires another (separate) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network (usually with the command prompt, Cygwin Window, or a Linux Terminal), telnet and login to _moonjelly_ with your standard MBARI password and type the following at the prompt: &nbsp;{color:red}{*}encryptCVSpw{*}{color}
This runs a script that outputs an encrypted version of your password.&nbsp; You may put any password in that you wish - even the same one as your standard MBARI network password.&nbsp; That is up to you.

Next, *{+}Please e-mail me the encrypted text (exactly as shown)+* so that I may add you to the repository password list.&nbsp; I will send you an e-mail when you are able to access the repository.

\\
&nbsp;

h3. *{+}CVS GUIs{+}*

GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2"&nbsp;link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. Please&nbsp;remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

Regards, - Karen A. Salamy (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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<property name="body"><![CDATA[h2.


----
*[*Welcome to CVS\!*|http://oceana:8081/display/CLT/Welcome+to+CVS%21]*

*[*Setting up a CVS Graphical User Interface (GUI)*|CLT:CVS Client Software Downloads^Setting up WinCVS_1.2_new.doc]*

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
&nbsp;]]></property>
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<property name="body"><![CDATA[----
h3. *{+}Welcome to CVS\!+*

CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp;&nbsp;Someone has&nbsp;requested that you be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

h3. \\


h3. +Permissions+

Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. _moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot for any reason, please let me know.

\\
&nbsp;

h3. +Password Access+

Access to the repository requires another (separate) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network (usually with the command prompt, Cygwin Window, or a Linux Terminal), telnet and login to _moonjelly_ with your standard MBARI password and type the following at the prompt: &nbsp;{color:red}{*}encryptCVSpw{*}{color}
This runs a script that outputs an encrypted version of your password.&nbsp; You may put any password in that you wish - even the same one as your standard MBARI network password.&nbsp; That is up to you.

Next, *{+}Please e-mail me the encrypted text (exactly as shown)+* so that I may add you to the repository password list.&nbsp; I will send you an e-mail when you are able to access the repository.

\\
&nbsp;

h3. *{+}CVS GUIs{+}*

GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2"&nbsp;link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. Please&nbsp;remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

Regards, - Karen A. Salamy (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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\\
&nbsp;

h3. *SmartSVN GUI Installation Files - Windows*

* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]\\
\\
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools

h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed. 

See [Maven At MBARI] for more details.

h3. Modelling with UML (Together)

After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

{warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN{code}{warning}

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 (tomcat version) from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

{note:Test Machine Installation Difference}
I also setup a test machine to help Alan Lash have something to develop against and for me to test somethings like using MS SQL Server instead of my SQL.  I will write notes where the instructions differ.
{note}

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 (tomcat version) from alfresco.org (the tar.gz file and moved it to /opt)
{note:Test Machine Installation Difference}
On the test machine, I installed Alfresco 2.1 tomcat version
{note}
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
{note:Test Machine Installation Difference}
I.S. was hoping to get Alfresco to run against the institutes MS SQL Server for support reasons so on the test machine, I used a database named 'Alfresco' on our database server solstice.shore.mbari.org.  Neil created the database for me and the user DB_Collaboration was used to access it.
{note}
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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<property name="body"><![CDATA[----
h3. *{+}Welcome to CVS\!+*

CVS is the MBARI Software Engineering source code repository which resides on the Linux server '{color:#3300ff}{_}moonjelly{_}{color}'.&nbsp;&nbsp;Someone has&nbsp;requested that you be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

h3. \\


h3. +Permissions+

Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. _moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot access _moonjelly_ for any reason, please let me know.

\\
&nbsp;

h3. +Password Access+

Access to the repository requires another (_separate_) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network (_usually with the command prompt, Cygwin Window, or a Linux Terminal_), {color:#3300ff}{*}telnet{*}{color} and login to _moonjelly_ with your standard MBARI password and type the following at the prompt: &nbsp;{color:red}{*}encryptCVSpw{*}{color}
This runs a script that outputs an encrypted version of your password.&nbsp; You may put any password in that you wish - even the same one as your standard MBARI network password.&nbsp; That is up to you.

Next, *{+}Please e-mail me the encrypted text (exactly as shown)+* so that I may add you to the repository password list.&nbsp; I will send you an e-mail when you are able to access the repository.

\\
&nbsp;

h3. *{+}CVS GUIs{+}*

GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the link [Setting up WinCVS_1.2|^Setting_up_WinCVS_1.2_new.doc]. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. Please&nbsp;remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

Regards, - Karen A. Salamy (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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<property name="body"><![CDATA[\\

There are&nbsp;two recommended CVS Clients to access the MBARI CVS Respository including:&nbsp;{color:#ff0000}{*}WinCVS{*}{color} and {color:#ff0000}{*}SmartCVS{*}{color}.&nbsp;&nbsp; Both clients work for all major operating systems including Windows, Macintosh, and Linux systems.&nbsp;The key bits of information to use when setting up either client are the following:
* {color:#0000cc}Your access method needs to be set to&nbsp;{color}{color:#0000cc}{*}pserver{*}{color}{color:#0000cc}&nbsp;{color}
* {color:#0000cc}User&nbsp; (Your MBARI user/e-mail&nbsp;account, e.g.,{color} {color:#0000cc}{_}salamy{_}{color}{color:#0000cc}){color}
* {color:#0000cc}Repository Server (MBARI CVS Repository is hosted on{color} {color:#0000cc}{*}{_}moonjelly{_}{*}{color}{color:#0000cc}){color}
* {color:#0000cc}CVSROOT ({color}{color:#0000cc}{*}_/home/cvs{_}{*}{color}{color:#0000cc}){color}

Thus, the full CVSROOT path for user _salamy_ would be:&nbsp;&nbsp;&nbsp; salamy@moonjelly:/home/cvs&nbsp;

----
\\

h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-7.0.2.zip|^smartcvs-win32-setup-nojre-7_0_2.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-7.0.2.tar.gz|^smartcvs-macosx-7_0_2.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-7.0.2.tar.gz|^smartcvs-generic-7_0_2.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}({color}{color:#0066cc}{*}NOTE:*{color}{color:#0066cc}&nbsp;Setup same for MacCVS and gCVS as well){color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS Getting-Started Tutorial|^smartcvs-tutorial.pdf] \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
&nbsp;]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

{note:title=Test Machine Installation Difference}
I also setup a test machine to help Alan Lash have something to develop against and for me to test somethings like using MS SQL Server instead of my SQL.  I will write notes where the instructions differ.  I setup the test machine on ssdsdevpc.shore.mbari.org which is an HP desktop machine running Fedora Core 7.
{note}

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 (tomcat version) from alfresco.org (the tar.gz file and moved it to /opt)
{note:title=Test Machine Installation Difference}
On the test machine, I installed Alfresco 2.1 tomcat version
{note}
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
{note:title=Test Machine Installation Difference}
I.S. was hoping to get Alfresco to run against the institutes MS SQL Server for support reasons so on the test machine, I used a database named 'Alfresco' on our database server solstice.shore.mbari.org.  Neil created the database for me and the user DB_Collaboration was used to access it.
{note}
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{tip}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{tip}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{tip}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{tip}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{tip}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{tip}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{tip}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{tip}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

{note:title=Test Machine Installation Difference}
I also setup a test machine to help Alan Lash have something to develop against and for me to test somethings like using MS SQL Server instead of my SQL.  I will write notes where the instructions differ.  I setup the test machine on ssdsdevpc.shore.mbari.org which is an HP desktop machine running Fedora Core 7.
{note}

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 (tomcat version) from alfresco.org (the tar.gz file and moved it to /opt)
{note:title=Test Machine Installation Difference}
On the test machine, I installed Alfresco 2.1 tomcat version
{note}
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
{note:title=Test Machine Installation Difference}
I.S. was hoping to get Alfresco to run against the institutes MS SQL Server for support reasons so on the test machine, I used a database named 'Alfresco' on our database server solstice.shore.mbari.org.  Neil created the database for me and the user DB_Collaboration was used to access it.
{note}
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
{note:title=Test Machine Installation Difference}
Fedora core 7 had 5.2.2 installed
{note}
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
{note:title=Test Machine Installation Difference}
I named the directory alfresco-2.1
{note}
# I then moved the tar into the alfresco-2.0 directory
{note:title=Test Machine Installation Difference}
alfreso-2.1 directory
{note}
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{tip}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{tip}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{tip}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{tip}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{tip}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{tip}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{tip}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{tip}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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<property name="body"><![CDATA[\\

There are&nbsp;two recommended CVS Clients to access the MBARI CVS Respository including:&nbsp;{color:#ff0000}{*}WinCVS{*}{color} and {color:#ff0000}{*}SmartCVS{*}{color}.&nbsp;&nbsp; Both clients work for all major operating systems including Windows, Macintosh, and Linux systems.&nbsp;The key bits of information to use when setting up either client are the following:
* User&nbsp; (Your MBARI user/e-mail&nbsp;account, e.g., _salamy_)
* Repository Server (MBARI CVS Repository is hosted on *{_}moonjelly{_}*)
* CVSROOT (*_/home/cvs{_}*)

Thus, the full CVSROOT path for user _salamy_ would be:&nbsp;&nbsp;&nbsp; salamy@moonjelly:/home/cvs&nbsp;

----
\\

h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-7.0.2.zip|^smartcvs-win32-setup-nojre-7_0_2.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-7.0.2.tar.gz|^smartcvs-macosx-7_0_2.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-7.0.2.tar.gz|^smartcvs-generic-7_0_2.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}({color}{color:#0066cc}{*}NOTE:*{color}{color:#0066cc}&nbsp;Setup same for MacCVS and gCVS as well){color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS Getting-Started Tutorial|^smartcvs-tutorial.pdf] \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
&nbsp;]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

{note:Test Machine Installation Difference}
I also setup a test machine to help Alan Lash have something to develop against and for me to test somethings like using MS SQL Server instead of my SQL.  I will write notes where the instructions differ.
{note}

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 (tomcat version) from alfresco.org (the tar.gz file and moved it to /opt)
{note:Test Machine Installation Difference}
On the test machine, I installed Alfresco 2.1 tomcat version
{note}
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
{note:Test Machine Installation Difference}
I.S. was hoping to get Alfresco to run against the institutes MS SQL Server for support reasons so on the test machine, I used a database named 'Alfresco' on our database server solstice.shore.mbari.org.  Neil created the database for me and the user DB_Collaboration was used to access it.
{note}
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{tip}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{tip}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{tip}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{tip}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{tip}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{tip}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{tip}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{tip}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

{note:title=Test Machine Installation Difference}
I also setup a test machine to help Alan Lash have something to develop against and for me to test somethings like using MS SQL Server instead of my SQL.  I will write notes where the instructions differ.
{note}

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 (tomcat version) from alfresco.org (the tar.gz file and moved it to /opt)
{note:title=Test Machine Installation Difference}
On the test machine, I installed Alfresco 2.1 tomcat version
{note}
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
{note:title=Test Machine Installation Difference}
I.S. was hoping to get Alfresco to run against the institutes MS SQL Server for support reasons so on the test machine, I used a database named 'Alfresco' on our database server solstice.shore.mbari.org.  Neil created the database for me and the user DB_Collaboration was used to access it.
{note}
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{tip}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{tip}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{tip}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{tip}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{tip}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{tip}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{tip}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{tip}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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<property name="body"><![CDATA[h2.


----
*[*Welcome to CVS\!*|http://oceana:8081/display/CLT/Welcome+to+CVS%21]*

*[*Setting up a CVS Graphical User Interface (GUI)*|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]*

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
&nbsp;]]></property>
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h3. *CVS Client&nbsp;Installation Files*

* [WinCVS-1.2.0.zip|~salamy:Helpful Software Downloads^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}

h3. &nbsp;


h3. CVS Client Set-Up Instructions

* [Setting up WinCVS-1.2.0.doc|^Setting up WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. &nbsp;


h3. CVS Administrative Information

* [CVS Admin Notes.doc|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
&nbsp;]]></property>
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<property name="body"><![CDATA[----
h3. *Welcome to CVS\!*

CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp;&nbsp;Someone has&nbsp;requested that you be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

h3. \\


h3. Permissions

Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. _moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot for any reason, please let me know.

\\
&nbsp;

h3. Password Access

Access to the repository requires another (separate) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network (usually with the command prompt, Cygwin Window, or a Linux Terminal), telnet and login to _moonjelly_ with your standard MBARI password and type the following at the prompt: &nbsp;{color:red}{*}encryptCVSpw{*}{color}
This runs a script that outputs an encrypted version of your password.&nbsp; You may put any password in that you wish - even the same one as your standard MBARI network password.&nbsp; That is up to you.

Next, *{+}Please e-mail me the encrypted text (exactly as shown)+* so that I may add you to the repository password list.&nbsp; I will send you an e-mail when you are able to access the repository.

\\
&nbsp;

h3. *CVS GUIs*

GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2"&nbsp;link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. Please&nbsp;remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

Regards, - Karen A. Salamy (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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<property name="body"><![CDATA[----
h3. *Welcome to CVS\!*

CVS is the MBARI Software Engineering source code repository which resides on the Linux server '_moonjelly_'.&nbsp;&nbsp;Someone has&nbsp;requested that you be added to&nbsp;a&nbsp;module (_project_)&nbsp;in the CVS repository.&nbsp;&nbsp;As a member of these modules, you will have access privileges to any current project whose {color:blue}{*}ownership{*}{color} or {color:blue}{*}group{*}{color} you belong to. If you need to be added to another module in the future, please let me know as I am the CVS system administrator for moonjelly (salamy@mbari.org).
\\

h3. \\


h3. *PERMISSIONS*

Permissions for these modules are set-up so that all files in the module are made writable only for members of the specified group.&nbsp; If someone is not part of a particular group, they will not have access to write to any files under that directory. These permissions are set recursively throughout
the project for security purposes. _moonjelly_ is on the NIS server at MBARI so you should be able to access the system through telnet via your main MBARI password.&nbsp;&nbsp; If you cannot for any reason, please let me know.

\\
&nbsp;

h3. *PASSWORD ACCESS*

Access to the repository requires another (separate) password.&nbsp; {color:red}{*}NOTE: To allow you access to the repository, I will need you to supply{*}{color} {color:red}{*}a cvs repository password.*{color}

To do this, access the MBARI network (usually with the command prompt, Cygwin Window, or a Linux Terminal), telnet and login to _moonjelly_ with your standard MBARI password and type the following at the prompt: &nbsp;{color:red}{*}encryptCVSpw{*}{color}
This runs a script that outputs an encrypted version of your password.&nbsp; You may put any password in that you wish - even the same one as your standard MBARI network password.&nbsp; That is up to you.

Next, *{+}Please e-mail me the encrypted text (exactly as shown)+* so that I may add you to the repository password list.&nbsp; I will send you an e-mail when you are able to access the repository.

\\
&nbsp;

h3. *CVS GUIs*

GUIs are the main way users interact with the repository to checkout, edit, and checkin files. Several of these include WinCVS (windows-based), gcvs (Linux-based), MacCVS (Mac-based) and SmartCVS (another windows-based version). You may also use the command line if you do not wish to use a GUI.&nbsp; I have written up a basic "getting started" document for repository users. At the moment, however, it outlines installing and working with WinCVS only since Windows is the main OS used at MBARI. I am not sure if you plan to use a GUI or command line. If you wish to try out WinCVS, please review the "Setting up WinCVS_1.2"&nbsp;link. You may also reference the guide should you wish to use the Linux version of the GUI, gcvs, as the menu structure is very similar for both GUIs.

The gcvs rpm can be downloaded for most RedHat systems from here: [http://rpm.pbone.net/index.php3/stat/4/idpl/1125012/com/gcvs-1.0-1.i386.rpm.html]

For the most in-depth cvs information, please see the CVS manual at: [http://www.cvshome.org/docs/manual/].

You can also simply "view" the current repository tree structure at: [http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/] .

{color:black}This will allow you to simply read any of the project modules.{color}&nbsp; Let me know how it works and if you have any problems. Please&nbsp;remember to send me your encrypted password as soon as possible.&nbsp;
&nbsp;

Regards, - Karen A. Salamy (_MBARI CVS administrator)_ \- salamy@mbari.org
\\]]></property>
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h3. *CVS Client&nbsp;Installation Files*

* [WinCVS-1.2.0.zip|~salamy:Helpful Software Downloads^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}

h3. &nbsp;


h3. CVS Client Set-Up Instructions

* [Setting up WinCVS-1.2.0.doc|^Setting up WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. &nbsp;


h3. CVS Administrative Information

* [CVS Admin Notes.doc|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

{note:title=Test Machine Installation Difference}
I also setup a test machine to help Alan Lash have something to develop against and for me to test somethings like using MS SQL Server instead of my SQL.  I will write notes where the instructions differ.  I setup the test machine on ssdsdevpc.shore.mbari.org which is an HP desktop machine running Fedora Core 7.
{note}

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 (tomcat version) from alfresco.org (the tar.gz file and moved it to /opt)
{note:title=Test Machine Installation Difference}
On the test machine, I installed Alfresco 2.1 tomcat version
{note}
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
{note:title=Test Machine Installation Difference}
I.S. was hoping to get Alfresco to run against the institutes MS SQL Server for support reasons so on the test machine, I used a database named 'Alfresco' on our database server solstice.shore.mbari.org.  Neil created the database for me and the user DB_Collaboration was used to access it.
{note}
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
{note:title=Test Machine Installation Difference}
Fedora core 7 had 5.2.2 installed
{note}
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
{note:title=Test Machine Installation Difference}
I named the directory alfresco-2.1
{note}
# I then moved the tar into the alfresco-2.0 directory
{note:title=Test Machine Installation Difference}
alfreso-2.1 directory
{note}
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
{note:title=Test Machine Installation Difference}
This was a bit different in FC7.  In order to get Xvfb installed I used "Add/Remove Software" to install it.  OpenOffice was already installed so I just had to find the soffice command location.  The command to get Xvfb running was also a bit different.  I had to create a ascii file called /etc/xvfb-auth.cfg that only had one line in it that read 'localhost'.  Then the command to start Xvfb was 'Xvfb :1 -auth /etc/xvfb-auth.cfg'.  Then I could start soffice the same way.  I changed the start_oo.sh file to reflect those commands.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
{note:title=Test Machine Installation Difference}
Did not do this
{note}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
{note:title=Test Machine Installation Difference}
/data/alfresco-2.1
{note}
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
{note:title=Test Machine Installation Difference}
This file already existed and was no different from the sample, so I skipped this step
{note}
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
{note:title=Test Machine Installation Difference}
This file already existed and so copied the original to custom-repository.properties.orig and edited the existing one.
{note}
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
{note:title=Test Machine Installation Difference}
I changed them to work with the MS SQL Server login so they looked like:
db.username=DB_Collaboration
db.password=********
db.pool.initial=10
db.pool.max=100
{note}
### Uncommented db.schema.update=true
{tip:title=Comment back out}
After the DB has been created (tables and such) you can comment this out to prevent DB changes in the future.
{tip}
### I commented out the two HSQL connection lines
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
{note:title=Test Machine Installation Difference}
Left the MySQL lines commented out, but uncommented the SQLServer lines and changed them to
db.driver=net.sourceforge.jtds.jdbc.Driver
db.url=jdbc:jtds:sqlserver://solstice.shore.mbari.org/Alfresco;domain=SHORE;user=DB_Collaboration;password=******
{note}
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
{note:title=Test Machine Installation Difference}
Already existed, so backuped up to .orig and edited to comment out the HSQL and uncomment the SQLServer one.
{note}
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
{note:title=Test Machine Installation Difference}
The downloaded alfresco already has the MySQL driver jar in the install, but since I am using SQLServer, I downloaded the jtds driver from the internet and installed the jtds-X.X.X.jar file in the /opt/alfresco-2.1/tomcat/common/lib to make it available to alfresco.
{note}
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0.  I also added the following line after the line that stated 'killall soffice.bin':
killall Xvfb.  That ensured the Xvfb process was killed when alfresco was shutdown.
{note:title=Test Machine Installation Difference}
Set it to /opt/alfresco-2.1/tomcat for the test machine
{note}
{tip}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{tip}
{note:title=Test Machine Installation Difference}
For the test machine, I wasn't too worried about details, so I skipped the next 15 or so steps (picks up again at configuring for MBARI LDAP below.
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{tip}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{tip}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{tip}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{tip}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponent" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
{note:title=Test Machine Installation Difference}
Did not setup SSL for the test machine
{note}
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{tip}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{tip}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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<property name="body"><![CDATA[h2.


----
h2.


h4. [*Welcome to CVS\!*|http://oceana:8081/display/CLT/Welcome+to+CVS%21][|http://oceana:8081/display/CLT/Welcome+to+CVS%21]

[*Setting up a CVS Graphical User Interface (GUI)*|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf][|http://oceana:8081/display/CLT/Welcome+to+CVS%21]


----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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<property name="body"><![CDATA[h2.


----
*[*Welcome to CVS\!*|http://oceana:8081/display/CLT/Welcome+to+CVS%21]*

*[*Setting up a CVS Graphical User Interface (GUI)*|http://oceana:8081/display/CLT/Welcome+to+CVS%21]*

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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<property name="body"><![CDATA[h2. [Welcome to CVS\!|http://oceana:8081/display/CLT/Welcome+to+CVS%21]


----
h2. [Setting up a CVS Graphical User Interface (GUI)|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]

\\

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

{note:title=Test Machine Installation Difference}
I also setup a test machine to help Alan Lash have something to develop against and for me to test somethings like using MS SQL Server instead of my SQL.  I will write notes where the instructions differ.  I setup the test machine on ssdsdevpc.shore.mbari.org which is an HP desktop machine running Fedora Core 7.
{note}

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 (tomcat version) from alfresco.org (the tar.gz file and moved it to /opt)
{note:title=Test Machine Installation Difference}
On the test machine, I installed Alfresco 2.1 tomcat version
{note}
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
{note:title=Test Machine Installation Difference}
I.S. was hoping to get Alfresco to run against the institutes MS SQL Server for support reasons so on the test machine, I used a database named 'Alfresco' on our database server solstice.shore.mbari.org.  Neil created the database for me and the user DB_Collaboration was used to access it.
{note}
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
{note:title=Test Machine Installation Difference}
Fedora core 7 had 5.2.2 installed
{note}
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
{note:title=Test Machine Installation Difference}
I named the directory alfresco-2.1
{note}
# I then moved the tar into the alfresco-2.0 directory
{note:title=Test Machine Installation Difference}
alfreso-2.1 directory
{note}
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
{note:title=Test Machine Installation Difference}
This was a bit different in FC7.  In order to get Xvfb installed I used "Add/Remove Software" to install it.  OpenOffice was already installed so I just had to find the soffice command location.  The command to get Xvfb running was also a bit different.  I had to create a ascii file called /etc/xvfb-auth.cfg that only had one line in it that read 'localhost'.  Then the command to start Xvfb was 'Xvfb :1 -auth /etc/xvfb-auth.cfg'.  Then I could start soffice the same way.  I changed the start_oo.sh file to reflect those commands.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
{note:title=Test Machine Installation Difference}
Did not do this
{note}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
{note:title=Test Machine Installation Difference}
/data/alfresco-2.1
{note}
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
{note:title=Test Machine Installation Difference}
This file already existed and was no different from the sample, so I skipped this step
{note}
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
{note:title=Test Machine Installation Difference}
This file already existed and so copied the original to custom-repository.properties.orig and edited the existing one.
{note}
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
{note:title=Test Machine Installation Difference}
I changed them to work with the MS SQL Server login so they looked like:
db.username=DB_Collaboration
db.password=********
db.pool.initial=10
db.pool.max=100
{note}
### Uncommented db.schema.update=true
### I commented out the two HSQL connection lines
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
{note:title=Test Machine Installation Difference}
Left the MySQL lines commented out, but uncommented the SQLServer lines and changed them to
db.driver=net.sourceforge.jtds.jdbc.Driver
db.url=jdbc:jtds:sqlserver://solstice.shore.mbari.org/Alfresco;domain=SHORE;user=DB_Collaboration;password=******
{note}
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
{note:title=Test Machine Installation Difference}
Already existed, so backuped up to .orig and edited to comment out the HSQL and uncomment the SQLServer one.
{note}
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
{note:title=Test Machine Installation Difference}
The downloaded alfresco already has the MySQL driver jar in the install, but since I am using SQLServer, I downloaded the jtds driver from the internet and installed the jtds-X.X.X.jar file in the /opt/alfresco-2.1/tomcat/common/lib to make it available to alfresco.
{note}
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note:title=Test Machine Installation Difference}
Set it to /opt/alfresco-2.1/tomcat for the test machine
{note}
{tip}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{tip}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{tip}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{tip}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{tip}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{tip}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{tip}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{tip}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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<property name="body"><![CDATA[h2.

----


h2. [Welcome to CVS\!|http://oceana:8081/display/CLT/Welcome+to+CVS%21]


----
h2. [Setting up a CVS Graphical User Interface (GUI)|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]

\\

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
&nbsp;]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

{note:title=Test Machine Installation Difference}
I also setup a test machine to help Alan Lash have something to develop against and for me to test somethings like using MS SQL Server instead of my SQL.  I will write notes where the instructions differ.  I setup the test machine on ssdsdevpc.shore.mbari.org which is an HP desktop machine running Fedora Core 7.
{note}

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 (tomcat version) from alfresco.org (the tar.gz file and moved it to /opt)
{note:title=Test Machine Installation Difference}
On the test machine, I installed Alfresco 2.1 tomcat version
{note}
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
{note:title=Test Machine Installation Difference}
I.S. was hoping to get Alfresco to run against the institutes MS SQL Server for support reasons so on the test machine, I used a database named 'Alfresco' on our database server solstice.shore.mbari.org.  Neil created the database for me and the user DB_Collaboration was used to access it.
{note}
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
{note:title=Test Machine Installation Difference}
Fedora core 7 had 5.2.2 installed
{note}
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
{note:title=Test Machine Installation Difference}
I named the directory alfresco-2.1
{note}
# I then moved the tar into the alfresco-2.0 directory
{note:title=Test Machine Installation Difference}
alfreso-2.1 directory
{note}
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
{note:title=Test Machine Installation Difference}
This was a bit different in FC7.  In order to get Xvfb installed I used "Add/Remove Software" to install it.  OpenOffice was already installed so I just had to find the soffice command location.  The command to get Xvfb running was also a bit different.  I had to create a ascii file called /etc/xvfb-auth.cfg that only had one line in it that read 'localhost'.  Then the command to start Xvfb was 'Xvfb :1 -auth /ect/xvfb-auth.cfg'.  Then I could start soffice the same way.  I changed the start_oo.sh file to reflect those commands.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
{note:title=Test Machine Installation Difference}
Did not do this
{note}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
{note:title=Test Machine Installation Difference}
/data/alfresco-2.1
{note}
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
{note:title=Test Machine Installation Difference}
This file already existed and was no different from the sample, so I skipped this step
{note}
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
{note:title=Test Machine Installation Difference}
This file already existed and so copied the original to custom-repository.properties.orig and edited the existing one.
{note}
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
{note:title=Test Machine Installation Difference}
I changed them to work with the MS SQL Server login so they looked like:
db.username=DB_Collaboration
db.password=********
db.pool.initial=10
db.pool.max=100
{note}
### Uncommented db.schema.update=true
### I commented out the two HSQL connection lines
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
{note:title=Test Machine Installation Difference}
Left the MySQL lines commented out, but uncommented the SQLServer lines and changed them to
db.driver=net.sourceforge.jtds.jdbc.Driver
db.url=jdbc:jtds:sqlserver://solstice.shore.mbari.org/Alfresco;domain=SHORE;user=DB_Collaboration;password=******
{note}
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
{note:title=Test Machine Installation Difference}
Already existed, so backuped up to .orig and edited to comment out the HSQL and uncomment the SQLServer one.
{note}
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{tip}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{tip}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{tip}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{tip}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{tip}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{tip}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{tip}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{tip}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

{note:title=Test Machine Installation Difference}
I also setup a test machine to help Alan Lash have something to develop against and for me to test somethings like using MS SQL Server instead of my SQL.  I will write notes where the instructions differ.  I setup the test machine on ssdsdevpc.shore.mbari.org which is an HP desktop machine running Fedora Core 7.
{note}

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 (tomcat version) from alfresco.org (the tar.gz file and moved it to /opt)
{note:title=Test Machine Installation Difference}
On the test machine, I installed Alfresco 2.1 tomcat version
{note}
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
{note:title=Test Machine Installation Difference}
I.S. was hoping to get Alfresco to run against the institutes MS SQL Server for support reasons so on the test machine, I used a database named 'Alfresco' on our database server solstice.shore.mbari.org.  Neil created the database for me and the user DB_Collaboration was used to access it.
{note}
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
{note:title=Test Machine Installation Difference}
Fedora core 7 had 5.2.2 installed
{note}
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
{note:title=Test Machine Installation Difference}
I named the directory alfresco-2.1
{note}
# I then moved the tar into the alfresco-2.0 directory
{note:title=Test Machine Installation Difference}
alfreso-2.1 directory
{note}
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
{note:title=Test Machine Installation Difference}
This was a bit different in FC7.  In order to get Xvfb installed I used "Add/Remove Software" to install it.  OpenOffice was already installed so I just had to find the soffice command location.  The command to get Xvfb running was also a bit different.  I had to create a ascii file called /etc/xvfb-auth.cfg that only had one line in it that read 'localhost'.  Then the command to start Xvfb was 'Xvfb :1 -auth /ect/xvfb-auth.cfg'.  Then I could start soffice the same way.  I changed the start_oo.sh file to reflect those commands.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{tip}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{tip}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{tip}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{tip}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{tip}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{tip}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{tip}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{tip}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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<property name="body"><![CDATA[h2.


----
h2. [Welcome to CVS\!|http://oceana:8081/display/CLT/Welcome+to+CVS%21]
\\


----
h2. [Setting up a CVS Graphical User Interface (GUI)|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]

\\

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

{note:title=Test Machine Installation Difference}
I also setup a test machine to help Alan Lash have something to develop against and for me to test somethings like using MS SQL Server instead of my SQL.  I will write notes where the instructions differ.  I setup the test machine on ssdsdevpc.shore.mbari.org which is an HP desktop machine running Fedora Core 7.
{note}

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 (tomcat version) from alfresco.org (the tar.gz file and moved it to /opt)
{note:title=Test Machine Installation Difference}
On the test machine, I installed Alfresco 2.1 tomcat version
{note}
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
{note:title=Test Machine Installation Difference}
I.S. was hoping to get Alfresco to run against the institutes MS SQL Server for support reasons so on the test machine, I used a database named 'Alfresco' on our database server solstice.shore.mbari.org.  Neil created the database for me and the user DB_Collaboration was used to access it.
{note}
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
{note:title=Test Machine Installation Difference}
Fedora core 7 had 5.2.2 installed
{note}
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
{note:title=Test Machine Installation Difference}
I named the directory alfresco-2.1
{note}
# I then moved the tar into the alfresco-2.0 directory
{note:title=Test Machine Installation Difference}
alfreso-2.1 directory
{note}
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
{note:title=Test Machine Installation Difference}
This was a bit different in FC7.  In order to get Xvfb installed I used "Add/Remove Software" to install it.  OpenOffice was already installed so I just had to find the soffice command location.  The rest of it was the same.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{tip}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{tip}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{tip}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{tip}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{tip}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{tip}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{tip}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{tip}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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<property name="body"><![CDATA[h3.

----


h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

{note:title=Test Machine Installation Difference}
I also setup a test machine to help Alan Lash have something to develop against and for me to test somethings like using MS SQL Server instead of my SQL.  I will write notes where the instructions differ.  I setup the test machine on ssdsdevpc.shore.mbari.org which is an HP desktop machine running Fedora Core 7.
{note}

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 (tomcat version) from alfresco.org (the tar.gz file and moved it to /opt)
{note:title=Test Machine Installation Difference}
On the test machine, I installed Alfresco 2.1 tomcat version
{note}
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
{note:title=Test Machine Installation Difference}
I.S. was hoping to get Alfresco to run against the institutes MS SQL Server for support reasons so on the test machine, I used a database named 'Alfresco' on our database server solstice.shore.mbari.org.  Neil created the database for me and the user DB_Collaboration was used to access it.
{note}
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
{note:title=Test Machine Installation Difference}
Fedora core 7 had 5.2.2 installed
{note}
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
{note:title=Test Machine Installation Difference}
I named the directory alfresco-2.1
{note}
# I then moved the tar into the alfresco-2.0 directory
{note:title=Test Machine Installation Difference}
alfreso-2.1 directory
{note}
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
{note:title=Test Machine Installation Difference}
This was a bit different in FC7.  In order to get Xvfb installed I used "Add/Remove Software" to install it.  OpenOffice was already installed so I just had to find the soffice command location.  The command to get Xvfb running was also a bit different.  I had to create a ascii file called /etc/xvfb-auth.cfg that only had one line in it that read 'localhost'.  Then the command to start Xvfb was 'Xvfb :1 -auth /etc/xvfb-auth.cfg'.  Then I could start soffice the same way.  I changed the start_oo.sh file to reflect those commands.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
{note:title=Test Machine Installation Difference}
Did not do this
{note}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
{note:title=Test Machine Installation Difference}
/data/alfresco-2.1
{note}
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
{note:title=Test Machine Installation Difference}
This file already existed and was no different from the sample, so I skipped this step
{note}
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
{note:title=Test Machine Installation Difference}
This file already existed and so copied the original to custom-repository.properties.orig and edited the existing one.
{note}
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
{note:title=Test Machine Installation Difference}
I changed them to work with the MS SQL Server login so they looked like:
db.username=DB_Collaboration
db.password=********
db.pool.initial=10
db.pool.max=100
{note}
### Uncommented db.schema.update=true
### I commented out the two HSQL connection lines
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
{note:title=Test Machine Installation Difference}
Left the MySQL lines commented out, but uncommented the SQLServer lines and changed them to
db.driver=net.sourceforge.jtds.jdbc.Driver
db.url=jdbc:jtds:sqlserver://solstice.shore.mbari.org/Alfresco;domain=SHORE;user=DB_Collaboration;password=******
{note}
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
{note:title=Test Machine Installation Difference}
Already existed, so backuped up to .orig and edited to comment out the HSQL and uncomment the SQLServer one.
{note}
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
{note:title=Test Machine Installation Difference}
The downloaded alfresco already has the MySQL driver jar in the install, but since I am using SQLServer, I downloaded the jtds driver from the internet and installed the jtds-X.X.X.jar file in the /opt/alfresco-2.1/tomcat/common/lib to make it available to alfresco.
{note}
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0.  I also added the following line after the line that stated 'killall soffice.bin':
killall Xvfb.  That ensured the Xvfb process was killed when alfresco was shutdown.
{note:title=Test Machine Installation Difference}
Set it to /opt/alfresco-2.1/tomcat for the test machine
{note}
{tip}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{tip}
{note:title=Test Machine Installation Difference}
For the test machine, I wasn't too worried about details, so I skipped the next 15 or so steps (picks up again at configuring for MBARI LDAP below.
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{tip}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{tip}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{tip}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{tip}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponent" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
{note:title=Test Machine Installation Difference}
Did not setup SSL for the test machine
{note}
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{tip}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{tip}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

{note:title=Test Machine Installation Difference}
I also setup a test machine to help Alan Lash have something to develop against and for me to test somethings like using MS SQL Server instead of my SQL.  I will write notes where the instructions differ.  I setup the test machine on ssdsdevpc.shore.mbari.org which is an HP desktop machine running Fedora Core 7.
{note}

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 (tomcat version) from alfresco.org (the tar.gz file and moved it to /opt)
{note:title=Test Machine Installation Difference}
On the test machine, I installed Alfresco 2.1 tomcat version
{note}
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
{note:title=Test Machine Installation Difference}
I.S. was hoping to get Alfresco to run against the institutes MS SQL Server for support reasons so on the test machine, I used a database named 'Alfresco' on our database server solstice.shore.mbari.org.  Neil created the database for me and the user DB_Collaboration was used to access it.
{note}
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
{note:title=Test Machine Installation Difference}
Fedora core 7 had 5.2.2 installed
{note}
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
{note:title=Test Machine Installation Difference}
I named the directory alfresco-2.1
{note}
# I then moved the tar into the alfresco-2.0 directory
{note:title=Test Machine Installation Difference}
alfreso-2.1 directory
{note}
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
{note:title=Test Machine Installation Difference}
This was a bit different in FC7.  In order to get Xvfb installed I used "Add/Remove Software" to install it.  OpenOffice was already installed so I just had to find the soffice command location.  The command to get Xvfb running was also a bit different.  I had to create a ascii file called /etc/xvfb-auth.cfg that only had one line in it that read 'localhost'.  Then the command to start Xvfb was 'Xvfb :1 -auth /etc/xvfb-auth.cfg'.  Then I could start soffice the same way.  I changed the start_oo.sh file to reflect those commands.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
{note:title=Test Machine Installation Difference}
Did not do this
{note}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
{note:title=Test Machine Installation Difference}
/data/alfresco-2.1
{note}
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
{note:title=Test Machine Installation Difference}
This file already existed and was no different from the sample, so I skipped this step
{note}
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
{note:title=Test Machine Installation Difference}
This file already existed and so copied the original to custom-repository.properties.orig and edited the existing one.
{note}
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
{note:title=Test Machine Installation Difference}
I changed them to work with the MS SQL Server login so they looked like:
db.username=DB_Collaboration
db.password=********
db.pool.initial=10
db.pool.max=100
{note}
### Uncommented db.schema.update=true
### I commented out the two HSQL connection lines
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
{note:title=Test Machine Installation Difference}
Left the MySQL lines commented out, but uncommented the SQLServer lines and changed them to
db.driver=net.sourceforge.jtds.jdbc.Driver
db.url=jdbc:jtds:sqlserver://solstice.shore.mbari.org/Alfresco;domain=SHORE;user=DB_Collaboration;password=******
{note}
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
{note:title=Test Machine Installation Difference}
Already existed, so backuped up to .orig and edited to comment out the HSQL and uncomment the SQLServer one.
{note}
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
{note:title=Test Machine Installation Difference}
The downloaded alfresco already has the MySQL driver jar in the install, but since I am using SQLServer, I downloaded the jtds driver from the internet and installed the jtds-X.X.X.jar file in the /opt/alfresco-2.1/tomcat/common/lib to make it available to alfresco.
{note}
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0.  I also added the following line after the line that stated 'killall soffice.bin':
killall Xvfb.  That ensured the Xvfb process was killed when alfresco was shutdown.
{note:title=Test Machine Installation Difference}
Set it to /opt/alfresco-2.1/tomcat for the test machine
{note}
{tip}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{tip}
{note:title=Test Machine Installation Difference}
For the test machine, I wasn't too worried about details, so I skipped the next 15 or so steps (picks up again at configuring for MBARI LDAP below.
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{tip}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{tip}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{tip}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{tip}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
{note:title=Test Machine Installation Difference}
Did not setup SSL for the test machine
{note}
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{tip}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{tip}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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<property name="body"><![CDATA[h2. [Welcome to CVS\!|CLT:Welcome to CVS!]


----
h2. [Setting up a CVS Graphical User Interface (GUI)|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]
\\

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
&nbsp;]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

{note:title=Test Machine Installation Difference}
I also setup a test machine to help Alan Lash have something to develop against and for me to test somethings like using MS SQL Server instead of my SQL.  I will write notes where the instructions differ.  I setup the test machine on ssdsdevpc.shore.mbari.org which is an HP desktop machine running Fedora Core 7.
{note}

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 (tomcat version) from alfresco.org (the tar.gz file and moved it to /opt)
{note:title=Test Machine Installation Difference}
On the test machine, I installed Alfresco 2.1 tomcat version
{note}
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
{note:title=Test Machine Installation Difference}
I.S. was hoping to get Alfresco to run against the institutes MS SQL Server for support reasons so on the test machine, I used a database named 'Alfresco' on our database server solstice.shore.mbari.org.  Neil created the database for me and the user DB_Collaboration was used to access it.
{note}
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
{note:title=Test Machine Installation Difference}
Fedora core 7 had 5.2.2 installed
{note}
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
{note:title=Test Machine Installation Difference}
I named the directory alfresco-2.1
{note}
# I then moved the tar into the alfresco-2.0 directory
{note:title=Test Machine Installation Difference}
alfreso-2.1 directory
{note}
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
{note:title=Test Machine Installation Difference}
This was a bit different in FC7.  In order to get Xvfb installed I used "Add/Remove Software" to install it.  OpenOffice was already installed so I just had to find the soffice command location.  The command to get Xvfb running was also a bit different.  I had to create a ascii file called /etc/xvfb-auth.cfg that only had one line in it that read 'localhost'.  Then the command to start Xvfb was 'Xvfb :1 -auth /etc/xvfb-auth.cfg'.  Then I could start soffice the same way.  I changed the start_oo.sh file to reflect those commands.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
{note:title=Test Machine Installation Difference}
Did not do this
{note}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
{note:title=Test Machine Installation Difference}
/data/alfresco-2.1
{note}
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
{note:title=Test Machine Installation Difference}
This file already existed and was no different from the sample, so I skipped this step
{note}
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
{note:title=Test Machine Installation Difference}
This file already existed and so copied the original to custom-repository.properties.orig and edited the existing one.
{note}
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
{note:title=Test Machine Installation Difference}
I changed them to work with the MS SQL Server login so they looked like:
db.username=DB_Collaboration
db.password=********
db.pool.initial=10
db.pool.max=100
{note}
### Uncommented db.schema.update=true
### I commented out the two HSQL connection lines
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
{note:title=Test Machine Installation Difference}
Left the MySQL lines commented out, but uncommented the SQLServer lines and changed them to
db.driver=net.sourceforge.jtds.jdbc.Driver
db.url=jdbc:jtds:sqlserver://solstice.shore.mbari.org/Alfresco;domain=SHORE;user=DB_Collaboration;password=******
{note}
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
{note:title=Test Machine Installation Difference}
Already existed, so backuped up to .orig and edited to comment out the HSQL and uncomment the SQLServer one.
{note}
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
{note:title=Test Machine Installation Difference}
The downloaded alfresco already has the MySQL driver jar in the install, but since I am using SQLServer, I downloaded the jtds driver from the internet and installed the jtds-X.X.X.jar file in the /opt/alfresco-2.1/tomcat/common/lib to make it available to alfresco.
{note}
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note:title=Test Machine Installation Difference}
Set it to /opt/alfresco-2.1/tomcat for the test machine
{note}
{tip}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{tip}
{note:title=Test Machine Installation Difference}
For the test machine, I wasn't too worried about details, so I skipped the next 15 or so steps (picks up again at configuring for MBARI LDAP below.
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{tip}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{tip}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{tip}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{tip}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
{note:title=Test Machine Installation Difference}
Did not setup SSL for the test machine
{note}
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{tip}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{tip}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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<property name="body"><![CDATA[h2. [Welcome to CVS\!|http://oceana:8081/display/CLT/Welcome+to+CVS%21][Welcome to CVS\!|CLT:Welcome to CVS!]


----
h2. [Setting up a CVS Graphical User Interface (GUI)|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]

\\

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
&nbsp;]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

{note:title=Test Machine Installation Difference}
I also setup a test machine to help Alan Lash have something to develop against and for me to test somethings like using MS SQL Server instead of my SQL.  I will write notes where the instructions differ.  I setup the test machine on ssdsdevpc.shore.mbari.org which is an HP desktop machine running Fedora Core 7.
{note}

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 (tomcat version) from alfresco.org (the tar.gz file and moved it to /opt)
{note:title=Test Machine Installation Difference}
On the test machine, I installed Alfresco 2.1 tomcat version
{note}
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
{note:title=Test Machine Installation Difference}
I.S. was hoping to get Alfresco to run against the institutes MS SQL Server for support reasons so on the test machine, I used a database named 'Alfresco' on our database server solstice.shore.mbari.org.  Neil created the database for me and the user DB_Collaboration was used to access it.
{note}
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
{note:title=Test Machine Installation Difference}
Fedora core 7 had 5.2.2 installed
{note}
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
{note:title=Test Machine Installation Difference}
I named the directory alfresco-2.1
{note}
# I then moved the tar into the alfresco-2.0 directory
{note:title=Test Machine Installation Difference}
alfreso-2.1 directory
{note}
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
{note:title=Test Machine Installation Difference}
This was a bit different in FC7.  In order to get Xvfb installed I used "Add/Remove Software" to install it.  OpenOffice was already installed so I just had to find the soffice command location.  The command to get Xvfb running was also a bit different.  I had to create a ascii file called /etc/xvfb-auth.cfg that only had one line in it that read 'localhost'.  Then the command to start Xvfb was 'Xvfb :1 -auth /etc/xvfb-auth.cfg'.  Then I could start soffice the same way.  I changed the start_oo.sh file to reflect those commands.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
{note:title=Test Machine Installation Difference}
Did not do this
{note}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
{note:title=Test Machine Installation Difference}
/data/alfresco-2.1
{note}
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
{note:title=Test Machine Installation Difference}
This file already existed and was no different from the sample, so I skipped this step
{note}
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
{note:title=Test Machine Installation Difference}
This file already existed and so copied the original to custom-repository.properties.orig and edited the existing one.
{note}
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
{note:title=Test Machine Installation Difference}
I changed them to work with the MS SQL Server login so they looked like:
db.username=DB_Collaboration
db.password=********
db.pool.initial=10
db.pool.max=100
{note}
### Uncommented db.schema.update=true
### I commented out the two HSQL connection lines
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
{note:title=Test Machine Installation Difference}
Left the MySQL lines commented out, but uncommented the SQLServer lines and changed them to
db.driver=net.sourceforge.jtds.jdbc.Driver
db.url=jdbc:jtds:sqlserver://solstice.shore.mbari.org/Alfresco;domain=SHORE;user=DB_Collaboration;password=******
{note}
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
{note:title=Test Machine Installation Difference}
Already existed, so backuped up to .orig and edited to comment out the HSQL and uncomment the SQLServer one.
{note}
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
{note:title=Test Machine Installation Difference}
The downloaded alfresco already has the MySQL driver jar in the install, but since I am using SQLServer, I downloaded the jtds driver from the internet and installed the jtds-X.X.X.jar file in the /opt/alfresco-2.1/tomcat/common/lib to make it available to alfresco.
{note}
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note:title=Test Machine Installation Difference}
Set it to /opt/alfresco-2.1/tomcat for the test machine
{note}
{tip}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{tip}
{note:title=Test Machine Installation Difference}
For the test machine, I wasn't too worried about details, so I skipped the next 15 or so steps (picks up again at configuring for MBARI LDAP below.
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{tip}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{tip}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{tip}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{tip}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{tip}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{tip}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://oceana.shore.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly
# TODO: Verify I know where the MySQL files are and that we can restore them correctly.  Also turn on binary logs and use a test machine to learn (and document here) how to restore from backup.

{warning:title=IMPORTANT}
For some strange reason, the Alfresco stack would seem to crash after 20-30 days of operation with some very cryptic errors.  I found some entries in the forums about changing the ulimit value in linux.  So I issued a 'ulimit -n 4096' and then restart Alfresco. I haven't seen that problem since.
{warning}]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools

h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed. See [Maven At MBARI] for more details.

h3. Modelling with UML (Together)

After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

{warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN{code}{warning}]]></property>
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<id name="id">3179448</id>
<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools

h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed. 

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool.  It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant.  You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory.

{note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above).  You can still use Together, but we are not eligible for upgrade/patches.
{note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

{warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN{code}{warning}

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI] ]]></property>
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<id name="id">880</id>
<property name="body"><![CDATA[h2. Adding your code to MBARI's repository

Here's the standard method of adding a new directory to the subversion repository.

1) On your local machine create the following directory structure
{noformat}
tempdir
`~~ myproject       <-- Replace 'myproject' with the name of your project
   `~~ tags
   `~~ branches
   `~~ trunk
      `~~ agent
      `~~ ctd2007
{noformat}

2) cd to _tempdir_ and run the following command
{{svn import myproject svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject}}

3) To check out _myproject's_ main trunk on another machine you run the command
{{svn co svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject/trunk myproject}}
{note:title:Be Careful}
Notice that we've added '/trunk' to the SVN URL above to check out only the trunk (main development line). If you omit '/trunk' you will check out all tags and branches as well as the trunk.
{note}

A free on-line guide to SVN is available at http://svnbook.red-bean.com/. The most useful svn commands are

{noformat}
svn status                            <-- shows you the status of files in your project
svn add some/new/file                 <-- add a new file to version control
svn del some/old/file                 <-- remove a file from version control
svn update                            <-- Get changes from the repository 
svn commit -m "some commit message"   <-- commit changes to the repository
svn help
{noformat}

If you find that you can't connect to the svn repository contact Karen Salamy. She may need to give you access permissions.
]]></property>
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<id name="id">879</id>
<property name="body"><![CDATA[h2. Adding your code to MBARI's repository

Here's the standard method of adding a new directory to the subversion repository.

1) On your local machine create the following directory structure
{noformat}
tempdir
`~~ myproject       <-- Replace 'myproject' with the name of your project
   `~~ tags
   `~~ branches
   `~~ trunk
      `~~ agent
      `~~ ctd2007
{noformat}

2) cd to _tempdir_ and run the following command
{{svn import myproject svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject}}

3) To check out _myproject's_ main trunk on another machine you run the command
{{svn co svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject/trunk myproject}}

A free on-line guide to SVN is available at http://svnbook.red-bean.com/. The most useful svn commands are

{noformat}
svn status                            <-- shows you the status of files in your project
svn add some/new/file                 <-- add a new file to version control
svn del some/old/file                 <-- remove a file from version control
svn update                            <-- Get changes from the repository 
svn commit -m "some commit message"   <-- commit changes to the repository
svn help
{noformat}

If you find that you can't connect to the svn repository contact Karen Salamy. She may need to give you access permissions.
]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">882</id>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">878</id>
<property name="body"><![CDATA[h2. Adding your code to MBARI's repository

Here's the standard method of adding a new directory to the subversion repository.

1) On your local machine create the following directory structure
{noformat}
tempdir
`~~ myproject <-- Replace 'myproject' with the name of your project
   `~~ tags
   `~~ branches
   `~~ trunk
      `~~ agent
      `~~ ctd2007
{noformat}

2) cd to _tempdir_ and run the following command
{{svn import TREX svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject}}

3) To check out _myproject's_ main trunk on another machine you run the command
{{svn co svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject/trunk myproject}}

A free on-line guide to SVN is available at http://svnbook.red-bean.com/. The most useful svn commands are

{noformat}
svn status   <-- shows you the status of files in your project
svn add some/new/file    <-- add a new file to version control
svn del some/old/file   <-- remove a file from version control
svn update   <-- Get changes from the repository 
svn commit -m "some commit message"   <-- commit changes to the repository
svn help
{noformat}

If you find that you can't connect to the svn repository contact Karen Salamy. She may need to give you access permissions.
]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">881</id>
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</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">877</id>
<property name="body"><![CDATA[h2. Adding your code to MBARI's repository

Here's the standard method of adding a new directory to the subversion repository.

1) On your local machine create the following directory structure
{panel}
tempdir
`~~ _myproject_ {color:red}<-- Replace 'myproject' with the name of your project{red}
   |~~ tags
   |~~ branches
   `~~ trunk
      |~~ agent
      `~~ ctd2007
{panel}

2) cd to _tempdir_ and run the following command
{{svn import TREX svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject}}

3) To check out _myproject's_ main trunk on another machine you run the command
svn co svn+ssh://kahuna.shore.mbari.org/svn/repos/myproject/trunk myproject

A free on-line guide to SVN is available at http://svnbook.red-bean.com/. The most useful svn commands are

svn status   <-- shows you the status of files in your project
svn add some/new/file    <-- add a new file to version control
svn del some/old/file   <-- remove a file from version control
svn update   <-- Get changes from the repository 
svn commit -m "some commit message"   <-- commit changes to the repository
svn help

If you find that you can't connect to the svn repository contact Karen Salamy. She may need to give you access permissions.
]]></property>
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<id name="id">10389198</id>
<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - http://www.cuahsi.org/
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools

h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed. See [Maven At MBARI] for more details.

h3. Modelling with UML (Together)

After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

{warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN{code}{warning}

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] ]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\
\\
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;http://kahuna.shore.mbari.org/viewvc/?root=svn\ .

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;http://kahuna.shore.mbari.org/viewvc/?root=svn\[\].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\
\\
\\
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;http://kahuna.shore.mbari.org/viewvc/?root=svn.

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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----
*[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21]*

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]*

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator (_Karen Salamy:&nbsp;_ salamy@mbari.org). Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ [_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]_)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
&nbsp;]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools

h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

[Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/], projects can be built without requiring the developer to check in  all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed. See [Maven At MBARI] for more details.

h3. Modelling with UML (Together)

After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

{warning:title=WarningTogether doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {code}{{$ cp Together_LINUX.BIN Together_LINUX.BIN.original}}
 {{$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN}}
 {{$ chmod u+x Together_LINUX.BIN}}
 {{$ ./Together_LINUX.BIN}}{code}{warning}]]></property>
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<property name="body"><![CDATA[h2.


----
*[*Welcome to CVS\!*|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21]*

*[*Setting up a CVS Graphical User Interface (GUI)*|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]**&nbsp;&nbsp;* *[*(Download .doc)*|CLT:CVS Client Software Downloads^Setting up WinCVS_1.2_new.doc]*

----
h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator (_Karen Salamy:&nbsp;_ salamy@mbari.org). Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname)_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}&nbsp;
\\
&nbsp;
\\ {color:blue}*&nbsp;*{color}

{color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}.{color}

{color:black}NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}&nbsp;{color:black}*&nbsp;*{color}

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
&nbsp;]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools

h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

[Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/], projects can be built without requiring the developer to check in  all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed. See [Maven At MBARI] for more details.

h3. Modelling with UML (Together)

After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

{warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN}}
$ chmod u+x Together_LINUX.BIN}}
$ ./Together_LINUX.BIN}}{code}{warning}]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools

h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

[Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/], projects can be built without requiring the developer to check in  all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed. See [Maven At MBARI] for more details.

h3. Modelling with UML (Together)

After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

{warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN{code}{warning}]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools

h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

[Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/], projects can be built without requiring the developer to check in  all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed. See [Maven At MBARI] for more details.

h3. Modelling with UML (Together)

After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

{warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {code}{{$ cp Together_LINUX.BIN Together_LINUX.BIN.original}}
 {{$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN}}
 {{$ chmod u+x Together_LINUX.BIN}}
 {{$ ./Together_LINUX.BIN}}{code}{warning}]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools

h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

[Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/], projects can be built without requiring the developer to check in  all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed. See [Maven At MBARI] for more details.

h3. Modelling with UML (Together)

After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

{warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {code}$ cp Together_LINUX.BIN Together_LINUX.BIN.original
 $ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN}}
 $ chmod u+x Together_LINUX.BIN}}
 $ ./Together_LINUX.BIN}}{code}{warning}]]></property>
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<property name="body"><![CDATA[\\
&nbsp;

----
h3. *SmartSVN GUI Installation Files - Windows*

* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]\\
\\
\\]]></property>
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h3. *CVS Client&nbsp;Installation Files*

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}

h3. &nbsp;


h3. CVS Client Set-Up Instructions

* [Setting up WinCVS-1.2.0.doc|^CVS_Source_Code_Repository.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. &nbsp;


h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
&nbsp;]]></property>
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&nbsp;

----
h3. *SmartSVN GUI Installation Files*


h3. *Windows*

* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]
* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})

\\
&nbsp;

h3. Macintosh

* [SmartSVN-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]

\\
&nbsp;

h3. Linux]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools

h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

[Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of this is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/], projects can be built without requiring the developer to check in  all the dependencies in local version control. Instead, the dependencies are fetch from the repository when they are needed. See [Maven At MBARI] for more details.

h3. Modelling with UML (Together)

After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

{warning:title=WarningTogether doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {code}{{$ cp Together_LINUX.BIN Together_LINUX.BIN.original}}
 {{$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN}}
 {{$ chmod u+x Together_LINUX.BIN}}
 {{$ ./Together_LINUX.BIN}}{code}{warning}]]></property>
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<property name="body"><![CDATA[\\
&nbsp;

----
h3. *SmartSVN GUI Installation Files*


h3. *Windows*

* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]
* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]\\
\\
\\

h3. Macintosh

\\

h3. Linux]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

[Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of this is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/], projects can be built without requiring the developer to check in  all the dependencies in local version control. Instead, the dependencies are fetch from the repository when they are needed. See [Maven At MBARI] for more details.

h3. Modelling with UML (Together)

After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

{warning:title=WarningTogether doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {code}{{$ cp Together_LINUX.BIN Together_LINUX.BIN.original}}
 {{$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN}}
 {{$ chmod u+x Together_LINUX.BIN}}
 {{$ ./Together_LINUX.BIN}}{code}{warning}]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">808</id>
<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Modelling with UML (Together)

After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

{warning:title=WarningTogether doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {code}{{$ cp Together_LINUX.BIN Together_LINUX.BIN.original}}
 {{$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN}}
 {{$ chmod u+x Together_LINUX.BIN}}
 {{$ ./Together_LINUX.BIN}}{code}{warning}]]></property>
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<property name="body"><![CDATA[\\
&nbsp;

----
h3. *SmartSVN GUI Installation Files*


h3. *Windows*

* SmartSVN-3.0.9.zip
* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]\\
\\
\\

h3. Macintosh
\\

h3. Linux]]></property>
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<property name="body"><![CDATA[h3. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool.  For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h3. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one.  Follow the templates of the other projects.  (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces.  Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h4. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page.  You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest.  (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page.  It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h4. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects.  Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry.  Use the blue navigation bar at the top to get back to Dashboard.  Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h4. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features.  It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account.  You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h4. Modelling with UML (Together)

After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product.  It appears Borland will be supporting the product vigorously, and the current version is recommended.

To install Together download one of the following:
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download.  After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose.

*Warning*: Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
 {panel}{{$ cp Together_LINUX.BIN Together_LINUX.BIN.original}}
 {{$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN}}
 {{$ chmod u+x Together_LINUX.BIN}}
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h3. *CVS Client&nbsp;Installation Files*

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}

h3. &nbsp;


h3. CVS Client Set-Up Instructions

* [Setting up WinCVS-1.2.0.doc|^Setting up WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. &nbsp;


h3. CVS Administrative Information

* [CVS Admin Notes.doc|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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h3. *CVS Client&nbsp;Installation Files*

* [WinCVS-1.2.0.zip|~salamy:Helpful Software Downloads^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}

h3. &nbsp;


h3. CVS Client Set-Up Instructions

* [Setting up WinCVS-1.2.0.doc|^Setting up WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. &nbsp;


h3. CVS Administrative Information

* [CVS Admin Notes.doc|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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h3. *CVS Client&nbsp;Installation Files*

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}

h3. &nbsp;


h3. CVS Client Set-Up Instructions

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. &nbsp;


h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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h3. *CVS Client&nbsp;Installation Files*

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}

h3. &nbsp;


h3. CVS Client Set-Up Instructions

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. &nbsp;


h3. CVS Administrative Information

* [CVS Admin Notes.doc|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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h3. *SmartSVN GUI Installation Files*


h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip] {color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]\\ \\

h3. Macintosh

* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

h3. Linux

* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp; ({color:#ff0000}Note: Requires JRE 1.4.1 or higher{color})]]></property>
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h3. *SmartSVN GUI Installation Files*

{noformat}

{noformat}

h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip] {color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]\\
\\

h3. Macintosh

* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

h3. Linux

* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp; ({color:#ff0000}Note: Requires JRE 1.4.1 or higher{color})]]></property>
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h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip] {color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]\\
\\

----
h3. Macintosh

* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp; ({color:#ff0000}Note: Requires JRE 1.4.1 or higher{color})]]></property>
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
&nbsp;
\\ {color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file.{color} {color:black}This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was immediately before you deleted it.{color}
{color:#000000}{*}Step 2:*{color} {color:#000000}Remove the file from your working copy of the directory. This can done by first{color} {color:black}highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color}
{color:#000000}{*}Step 3:*{color} {color:#000000}Indicate to CVS that you want to delete the file. This can done in WinCVS by first{color} {color:black}highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}{color:#000000}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}
\\

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}. NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}
\\

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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&nbsp;

----
h3. *SmartSVN GUI Installation Files*


h3. *Windows*

* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]
* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})\\

h3. Macintosh

* [SmartSVN-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]

\\
&nbsp;

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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
&nbsp;
\\ {color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:
*Step 1:* Make sure that you have not made any uncommitted modifications to the file.{color} {color:black}This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was immediately before you deleted it.{color}{color:blue}
*Step 2:* Remove the file from your working copy of the directory. This can done by first{color} {color:black}highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color}{color:blue}
*Step3:* Indicate to CVS that you want to delete the file. This can done in WinCVS by first{color} {color:black}highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}{color:blue}Step 4:{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}
\\

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}. NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}
\\

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
&nbsp;]]></property>
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&nbsp;

----
h3. *SmartSVN GUI Installation Files*


h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]
* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]\\

h3. Macintosh

* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\

h3. Linux

({color:#ff0000}Note: Requires JRE 1.4.1 or higher{color})
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]]]></property>
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h3. *SmartSVN GUI Installation Files*


h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]
* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]\\ \\

h3. Macintosh

* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\ \\

h3. Linux

({color:#ff0000}Note: Requires JRE 1.4.1 or higher{color})
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]]]></property>
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h3. *SmartSVN GUI Installation Files*


h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]
* [SmartSVN-3.0.7.zip|SVN Client Software Downloads^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|SVN Client Software Downloads^SmartSVN.zip]\\
\\ \\

h3. Macintosh

* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\ \\

h3. Linux

({color:#ff0000}Note: Requires JRE 1.4.1 or higher{color})
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

See [SVN at MBARI] for more details.

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
&nbsp;
\\ {color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:{color}
{color:black}{*}Step 1:*{color} {color:black}Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was&nbsp;{color} {color:black}immediately before you deleted it.{color}
{color:black}{*}Step 2:*{color} {color:black}Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}Selection.{color}
{color:black}{*}Step 3:*{color} {color:black}Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}
{color:black}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}
\\

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}. NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}
\\

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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<property name="body"><![CDATA[h3. Download and Install Client&nbsp;

To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp; \\

h3. Setting up SmartSVN to see the SVN repository on Kahuna
\\ \\]]></property>
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
&nbsp;
\\ {color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:
*Step 1:* Make sure that you have not made any uncommitted modifications to the file. This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was immediately before you deleted it.
*Step 2:* Remove the file from your working copy of the directory. This can done by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.
*Step 3:* Indicate to CVS that you want to delete the file. This can done in WinCVS by first highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.
*Step 4:* Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}
\\

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}. NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}
\\

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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<property name="body"><![CDATA[h2. Adding your code to MBARI's CVS Source Code Repository

Here's the standard method of operatation for working with the CVS GUI clients.&nbsp;
\\
\\ {color:blue}{*}Creating a project:&nbsp;*{color} Due to the need for proper organization of files and file permissions, ALL projects (_not including subdirectories_) in the CVS repository on moonjelly are to be set-up by the repository administrator. Set-up involves creating project groups to restrict unauthorized users from editing or destroying files. New repository projects (modules) are generally set-up at the request of project managers, although any person who wishes to use the repository can make a request for a new project. To have a project (module) created, please e-mail the desired project name and list of users who will need access to the CVS administrator (salamy@mbari.org). Examples of previous projects are _tiburon_, _isi_, _nmc_.
\\

{color:blue}{*}Checking out a module:*{color} To check out a module (project or folder) in the repository, click *Create* on main menu then click *Checkout Module...*. In the checkout module section, type in the module name you will be working with (no need to indicate /home/cvs). If this is a new project with no previous files in it or if you wish to check out all files in a project, check out the project (e.g., new project name "toolsled" - type in the word _toolsled_). If you desire a particular subdirectory already created in a project enter the following (_projectname/subdirectoryname_, OR, to checkout an ndividual file from that project, enter (_projectname/subdirectoryname/filename_). The latter will checkout the one file and all listed subdirectories. Be sure to set your home directory before checking files out as the default is to place all files on your computer's hard drive. If this works, you should see the GUI display folders and files checked out. Folders will be in orange, while files will be shown in green.&nbsp; Note: If you plan to work on files in your home directory that you already checked out previously, it is a good idea to first update the copy with the most recent version in the CVS repository. This is important as the file may have been edited by another group user since you last worked on it. To Update a project, folder or file in your home directory, simply click on the directory item and then on the menu bar click *Modify - Update Selection*. You may also click on the user interface button (white rectangle with a downward pointing green arrow). The WinCVS command line will show file and folder updates.
\\

{color:blue}{*}Adding files to a project.*{color} In CVS, users edit and create new files in their home directory (a.k.a. a working directory or sandbox). _To set up your home directory see_ _[_Setting up WinCVS-1.2.pdf_|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf]__)._
To add a new file to a directory, follow these steps:
*Step 1:* You must first have a working copy of the directory.
*Step 2:* Create the new file(s) inside your checked-out working copy of the directory.
*Step 3:* In WinCVS, use the explore window (usually in left upper corner of screen) to browse to your home directory and view the new file(s) you have added.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Click the new file(s) with your mouse and add the file(s) by either:&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Add Selection*. If the file contains binary data click *Modify - Add Selection Binary*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}_
*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)* Clicking on the user interface button (white rectangle with a red "plus" sign on it). If the file is a binary, click the binary add button which is white with a red "plus" sign and 01 on it.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
*Step 4:* Commit the selection. This step actually "Adds" (checks-in) the file(s) to the repository. This can either be done with the file menu or with the user interface button.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *1)* Clicking on menu bar *Modify - Commit Selection*
_&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_ _{+}OR{+}{_}{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2)*{color} {color:black}Clicking on the user interface button (white rectangle with a red arrow pointing{color} {color:black}left on it).{color}
{color:black}*&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*{color}
{code}
NOTE: (Holding the shift key down allows the addition of more than one file at a time).
{code}
&nbsp;{color:black}{*}You can also add new directories to a project.*{color} {color:black}However, you must first add the directory{color} {color:black}in a separate step before adding any files to it. Unlike other CVS commands, the{color} {color:black}{*}{_}add{_}{*}{color} {color:black}options{color} {color:black}are not recursive.{color}
\\
&nbsp;
\\ {color:blue}{*}Removing files from a project.*{color} {color:black}To remove a file, but remain able to retrieve old revisions{color} {color:black}follow these steps:
*Step 1:* Make sure that you have not made any uncommitted modifications to the file.  This can be done by using the{color} {color:black}{*}{_}diff{_}{*}{color} {color:black}command. You can also use the{color} {color:black}{*}{_}status{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color} {color:black}commands. If you remove the file without committing your changes, you{color} {color:black}will not be able to retrieve the file as it was immediately before you deleted it.{color}
{color:#000000}{*}Step 2:*{color} {color:#000000}Remove the file from your working copy of the directory. This can done by first{color} {color:black}highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color}
{color:#000000}{*}Step 3:*{color} {color:#000000}Indicate to CVS that you want to delete the file. This can done in WinCVS by first{color} {color:black}highlighting the file and then clicking the main menu item{color} {color:black}{*}Modify - Remove{*}{color} {color:black}{*}Selection.*{color} {color:black}CVS should then highlight the file in red.{color}{color:#000000}{*}Step 4:*{color} {color:black}Remove the file from the repository. Click the commit GUI button or click on{color} {color:black}menu bar{color} {color:black}{*}Modify - Commit Selection{*}{color}{color:black}.{color}
\\

{color:black}When you commit the removal of the file, CVS records the fact that the file no longer exists. It is{color} {color:black}possible for a file to exist on only some branches and not on others, or to re-add another file with{color} {color:black}the same name later. CVS will correctly create or not create the file, based on the revision{color} {color:black}number or date options specified during{color} {color:black}{*}{_}checkout{_}{*}{color} {color:black}or{color} {color:black}{*}{_}update{_}{*}{color}{color:black}. NOTE: When you remove a file, it{color} {color:black}is removed only on the branch that you are working on. You can later merge the removals to{color} {color:black}another branch if you want.{color}
\\

{color:black}{*}You can also remove directories from a project{*}{color}{color:black}. The concept of removing directories is{color} {color:black}similar to removing files - you want the directory to not exist in your current working{color} {color:black}directories, but you also want to be able to retrieve old releases in which the directory{color} {color:black}existed.{color} {color:black}The way that you remove a directory is to remove all files in it. You do not remove the{color} {color:black}directory itself; there is no way to do that. Instead you specify the "prune empty directories"{color} {color:black}option to and update or checkout. This will cause CVS to remove empty directories from{color} {color:black}working directories. Probably the best way to do this is to always specify "prune empty{color} {color:black}directories". If you want and empty directory then put a dummy file (e.g., '.keepme') in it to{color} {color:black}prevent the "prune empty directories" option from removing it.{color}
\\ {color:black}It is best to become familiar with the WinCVS GUI and its checkout options before working in the{color} {color:black}repository. WinCVS has a "Help" menu that is useful. For more in-depth information, go to the{color} {color:black}CVS main web page{color} {color:blue}[http://www.cvshome.org/]{color} {color:black}and download the CVS manual.{color}
\\
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h3. *CVS Client&nbsp;Installation Files*

* [WinCVS-1.2.0.zip|~salamy:Helpful Software Downloads^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}

h3. &nbsp;


h3. CVS Client Set-Up Instructions

* [Setting up WinCVS-1.2.0.pdf|~salamy:Helpful Software Downloads^Setting up WinCVS_1 2.pdf] *\-* {color:#0066cc}{*}Windows{*}{color}\\

h3. &nbsp;


h3. CVS Administrative Information

* [CVS Admin Notes.doc|~salamy:Helpful Software Downloads^CVS Source Code Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;http://kahuna.shore.mbari.org/viewvc/?root=svn\[\].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">3670045</id>
<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
\\
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\
\\
\\
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;http://kahuna.shore.mbari.org/viewvc/?root=svn\[\].

See [SVN at MBARI] for more details.

\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">3670046</id>
<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
\\
\\
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\
\\
\\
\\
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;http://kahuna.shore.mbari.org/viewvc/?root=svn\[\].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">3637281</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">3670043</id>
<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;http://kahuna.shore.mbari.org/viewvc/?root=svn[].

See [SVN at MBARI] for more details.

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit the MBARI [Project Development page|http://oceana.shore.mbari.org].

All of these environments are only visible inside MBARI at this time. An action item (low priority) is to investigate whether selected environments can be made visible outside MBARI.

Contact Kevin Gomes with questions or permission requests for certain tools or spaces.

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.

h2. The Tools


h3. Content Management ([Alfresco|http://oceana.shore.mbari.org:8080/alfresco])

[Deployment Information]
[Installation Notes]
[alfresco.mbari.org Installation Notes]
[alfresco-test.shore.mbari.org Installation Notes]

Alfresco is intended to replace the Project Library on Tornado as the repository for MBARI project documents. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password) to see the project library materials. The default initial page (when logged in) shows several folders, but only the Project Library folder is of interest. (You may need to change the default items per page to see all the projects in one view.)

To create a short cut to the Project Library, enter that folder. Then select
More Actions/View Details, then "Create Shortcut" (on the right side fo the page).

(It is not clear how to make this the default home page. It is also not clear how to link directly to Alfresco content. This information will be added when available.)

h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts a Maven repository at [http://oceana.shore.mbari.org/maven2]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modelling with UML (JBuilder 2007 Enterprise)

In 2007, we decided to move from Together modeling tool to the JBuilder tool. It still uses the Together engine, but has a much better roadmap and Together was VERY stagnant. You can download JBuilder 2007 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded, you need to install the following [.slip|https://oceana.shore.mbari.org:8443/alfresco/download/attach/workspace/SpacesStore/9068968b-6bb8-11dc-ad56-2daf5cfa9d9b/concurrent_28136.slip] file in the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}
After reviewing existing modelling tools, the SDS group selected Together as their tool of choice. Together has previously been used for UML modelling at MBARI, but was not kept up to date when Borland bought the product. It appears Borland will be supporting the product vigorously, and the current version is recommended.
To install Together download one of the following:
\\
\\
\\
\\
\\
\\
# [Together For Windows|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Borland%20Together%20for%20Windows.exe]
# [Together For OSX |http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_OSX.ZIP]
# [Together For LINUX|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/Together_LINUX.BIN]

Install the download. After installing, download the license file:
# [concurrent_24267.slip|http://oceana.shore.mbari.org:8080/alfresco/webdav/ProjectLibrary/Collaboration%20Tools/Borland%20Together/concurrent_24267.slip]

and put in the (Together Install Directory)/license directory. If you need to check out a license for offline use, or have any other questions, contact Kevin Gomes.

We intend to provide some links to pages describing the various tools available and information about why we chose the ones we chose. {warning:title=Warning}Together doesn't always install nicely on some Linux distros. If you run the installer and get an error that mentions libc.s0.6 and libpthreads.so.0 problems etc, go (i.e. cd) to the directory where you extracted the downloaded file and:
{code}
$ cp Together_LINUX.BIN Together_LINUX.BIN.original
$ cat Together_LINUX.BIN.original \| sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Together_LINUX.BIN
$ chmod u+x Together_LINUX.BIN
$ ./Together_LINUX.BIN
{code}{warning}
\\
\\
\\
\\
\\

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;http://kahuna.shore.mbari.org/viewvc/?root=svn\[\].

See [SVN at MBARI] for more details.\\

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[We had some experience with a product called Together Control Center from TogetherSoft.  TogetherSoft was then purchased by Borland and they really managed to mess it up.  It was really behind (no UML 2.0) support and was in dire need of an update.  Borland tried to release it as an Eclipse product and it really did not work well. So we started to look around.  Right around the time I started investigating other UML Tools, Borland came out with Together 2006 For Eclipse.  So to give it a fair shake, we tried several tools (I found a fairly good tool/feature matrix at [http://www.oose.de/umltools.htm]:

* [Artisan Studio]
* [Borland's Together]
* [IBM Rational Software Architect]
* [Oracle JDeveloper]
* [MagicDraw]
* [Omondo]
* [VisualParadigm]

Turns out the OOI group was interested in a similar tool, but had to have some special features like SysML and State Diagrams.  I looked up SysML and there was a short list of tools supporting SysML:

* MDG Technology for SysML (Sparx Systems)
** SysML Support: Sparx provides a plug-in to their popular and award-winning UML 2.x modeling tool, Enterprise Architect (EA), that supports the OMG SysML 1.0 specification. Consequently, you will need Enterprise Architect 6.5 to run this plug-in. However, both EA and the SysML plug-in are reasonably priced, so you will likely find this combination an outstanding value when you compare it with the competition.
* Artisan Studio (Artisan Software)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* SysML Toolkit (EmbeddedPlus)
** SysML Support: Embedded Plus provides a SysML plug-in for IBM's Rational Software Development Platform. Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* Rhapsody v. 6.1 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.
* TAU G2 v. 2.6 (Telelogic)
** SysML Support: Supports some early version of SysML; not clear when the product will be updated to support OMG SysML 1.0.

Decision Matrix

||Tool Name||Windows||LINUX||Mac OSX||UML Version (1.X/2.X)||SysML Support||State Diagrams||Languages||IDE Integration||Roundtrip||Code Generation||Target Platforms||Comments||Cost||
|[Apollo|http://www.gentleware.com/products.html]| | | | | | | | |Eclipse|Only for Java|Java,C++|Currently only supports Class diagrams ... ouch!|Subscription: $56/year|
|[Artisan Studio|http://www.artisansw.com/products]|(/)|(x)|(x)|2.X|(/)|(/)|C, C++, Java, Ada, Spark Ada|(x)|(?)|(/)|VxWorks and Win32|Not a very professional install. Could not get working to test (see [Artisan Studio]).|(?)|
|[Borland Together|http://www.borland.com/us/products/together/index.html]|(/)|(/)|(/)|2.0|(x)|(/)|Java,C++|Eclipse|(/) The best by far|(/) Java,C++|(?)|After getting the license hell worked out, I tried to just create some simple models, but I could not change associations by right clicking on them and if you use link templates and tried to change them, the links would disappear! OK, I figured a way around that and you need to delete the old and create a new. After that, everything looks pretty good.|$1500 (this has a back support penalty so the first round would cost $3000, then $1500 each year after that)|
|[Embedded Plus|http://www.embeddedplus.com/SysML.php]| | | | | | | | | | | | | |
|[IBM Rational Rose Technical Developer|http://www-306.ibm.com/software/awdtools/developer/technical]| | | | | | | | | | | | | |
|[IBM Rational Software Architect|http://www-128.ibm.com/developerworks/rational/products/rsa]| | | | | | | | | | | |Still have not gotten license issues cleared up so have not been able to test|$5500/$9625 float|
|[JDeveloper|http://www.oracle.com/technology/products/jdev/index.html]| | | | | | | | | | | | | |
|[MagicDraw|http://www.magicdraw.com]|(/)|(/)|(/)|2.1|(/)|(/)|Java/J2EE, C#, C++, CORBA IDL, .NET, XML Schema, WSDL, Database Schema, DDL Generation|(?)|Yes for Java and C++|Yes, same list as Languages|(?)|I got it up and running.  It does not generate all the clean of HTML and I could not get the roundtrip engineering to work very well.  The option to refresh the code set was greyed out so I could not synch up the code.|This is a bit involved.  I figured we would want Enterprise mobile licenses as this allows on user to have it on three machines.  Todd Anderson bought two licenses in 1999, so we could upgrade them for $1906 (that is for both).  New mobile licenses are $1799 for locked and $2540 for concurrent.  We will most likely get academic pricing which takes of %40 so that would end up as $1079 each for locked and $1524 floating.  Maintence for new would also tack on $300 for each license. SysML and DODAF plugins cost extra and would be about $549 for both (each license).|
|[Omondo|http://www.omondo.com]| | | | | | | | | | | | | |
|[Posiedon|http://www.gentleware.com/products.html]| | | | | | | | |(x)|Java only|Java, C++, C#, CORBA IDL, Delphi, Perl, PHP4, SQL DDL, VB.NET|In using the interface several menus and componetns just dissappear almost making it unuseable ... UG!|Standard:$249,Professional:$875 locked/$1549 concurrent,Embedded Enterprise:$3590|
|[PragmaDev|http://www.pragmadev.com]| | | | | | | | | | | | | |
|[Rhapsody|http://www.ilogix.com/sublevel.aspx?id=53]| | | | | | | | | | | | | |
|[SmartDraw|http://www.smartdraw.com/exp/srd]| | | | | | | | | | | | | |
|[Sparx|http://www.sparxsystems.com]|(/)|(/)|(x)|2.1|Yes, with MDG|(/)|C++, Java, C#, VB.Net, Visual Basic, Delphi, PHP, Python and ActionScript|Visual Studio and Eclipse|Yes, but I don't think automatically|Y|(?)|There are two pieces, Enterprise Architect(EA) and MDG Technology for SysML.  EA covers UML and MDG adds in SysML support. This one along with Borland one the Jolt award for 2006 for productivity. The EA tools did not really handle code well. Associations with multiplicity did not generate code correctly.|EA=$239,MDG=$100|
|[TAU|http://www.telelogic.com/products/tau/index.cfm]| | | | | | | | | | | | | |
|[Umbrello|http://uml.sourceforge.net/index.php]| | | | | | | | | | | | | |
|[VisualParadigm|http://www.visual-paradigm.com/product/vpsuite]|(/)|(/)|(/)|2.X|Looks like they support certain aspects of SysML|(/)|Instant Reverse Engineering on Java Source, Java Class, C++ Source, .NET DDL or EXE files, CORBA IDL Source, Ada 9x Source, XML, XML Schema, JDBC, Hibernate, PHP 5.0 Source. Instant Code Generator on Java Source, C# Source, VB .NET Source, PHP Source, ODL, ActionScript Source, IDL Source, C++ Source, Delphi Source, Perl Source, XML Schema, Python Source, and Objective-C Source|Eclipse, NetBeans, InteliJ, JDeveloper, Visual Studio, JBuilder, SunONE, Web Logic|(/)|(/)| |I had some issues when running in Eclipse when I had other packages like MyEclipse pointing to the same Eclipse.  When I useda  clean Eclipse install, seemed to work great. Has a bunch of other tools like DB, etc. that I really did not try out. Associations did not generate code! Awaiting techincal support. I did hit what might be a show stopper. When specifying associations of multiplicity, you cannot specify how you want the multiplicity generated in code (Collection, Vector, Array, etc.).  This is a HUGE issue! Yep, I confirmed it.  You can tell the code generator what kind of collection you wish to use in the UML tool, but in SDE you cannot specify, it always uses object arrays (ouch!). So much for VP.|$1750 (no maint.)|
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AMQP: Advanced Message Queuing Protocol - [http://www.amqp.org]
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ARI-WG: Access to Remote Instrumentation in a distributed environment - Working Group. OpenGrid Forum [http://www.ogf.org/gf/group_info/view.php?group=ari-wg]
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# HDF: Hierarchical Data Format
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# JVM: Java Virtual Machine - http://en.wikipedia.org/wiki/Jvm
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MB/CA Current: a MBARI project in 2011
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# ODSS: Oceanographic Decision Support System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOI CI: Ocean Observatories Initiative CyberInfrastructure: [http://ci.oceanobservatories.org/] (Developers site: [http://ooici.net/])
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software).
# SCPI: Self Contained Plankton Imager, an MBARI project in 2011
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WCS: Web Coverage Service
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">19038610</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">15664200</id>
<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# {color:#0000ff}MB/CA Current: a MBARI project in 2011{color}
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOI CI: Ocean Observatories Initiative CyberInfrastructure: [http://ci.oceanobservatories.org/] (Developers site: [http://ooici.net/])
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software Integration).
# {color:#0000ff}SCPI:&nbsp; Self Contained Plankton Imager, an MBARI project in 2011{color}
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">15631449</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">15664198</id>
<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOI CI: Ocean Observatories Initiative CyberInfrastructure: [http://ci.oceanobservatories.org/] (Developers site: [http://ooici.net/])
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software Integration).&nbsp;
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. http://www.w3.org/
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AMQP: Advanced Message Queuing Protocol - http://www.amqp.org
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ARI-WG: Access to Remote Instrumentation in a distributed environment - Working Group. OpenGrid Forum [http://www.ogf.org/gf/group_info/view.php?group=ari-wg]
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# HDF: Hierarchical Data Format
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MB/CA Current: a MBARI project in 2011
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# ODSS: Oceanographic Decision Support System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOI CI: Ocean Observatories Initiative CyberInfrastructure: [http://ci.oceanobservatories.org/] (Developers site: [http://ooici.net/])
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software).
# SCPI: Self Contained Plankton Imager, an MBARI project in 2011
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WCS: Web Coverage Service
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">18252553</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10945014</id>
<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# <!--  /* Font Definitions */ @font-face 	{font-family:Arial; 	panose-1:2 11 6 4 2 2 2 2 2 4; 	mso-font-charset:0; 	mso-generic-font-family:auto; 	mso-font-pitch:variable; 	mso-font-signature:3 0 0 0 1 0;}  /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal 	{mso-style-parent:""; 	margin:0in; 	margin-bottom:.0001pt; 	mso-pagination:widow-orphan; 	font-size:12.0pt; 	font-family:"Times New Roman"; 	mso-fareast-font-family:"Times New Roman"; 	mso-bidi-font-family:"Times New Roman";} a:link, span.MsoHyperlink 	{color:blue; 	text-decoration:underline; 	text-underline:single;} a:visited, span.MsoHyperlinkFollowed 	{mso-style-noshow:yes; 	color:purple; 	text-decoration:underline; 	text-underline:single;} @page Section1 	{size:8.5in 11.0in; 	margin:1.0in 1.25in 1.0in 1.25in; 	mso-header-margin:.5in; 	mso-footer-margin:.5in; 	mso-paper-source:0;} div.Section1 	{page:Section1;} -->CENIC: The Corporation for Education Network Initiatives in California&nbsp; http://www.cenic.org/
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.&nbsp;

To use SVN first requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org). {color:#ff0033}{*}NOTE:*{color} {color:#ff0033}In the rare event the administrator is on vacation or unavailable, please&nbsp;submit your&nbsp;SVN request to the IS Remedy page at:&nbsp;{color} [https://ishelp.shore.mbari.org/helpdesk/WebObjects/Helpdesk] {color:#ff0033}and it will be assigned by IS appropriately based on urgency level.{color}

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

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[SVN Client Software Downloads|CLT:SVN Client Software Downloads] {color:#ff0000}\- Windows, Macs, Linux Systems{color}

[Setting up SVN Client&nbsp;to MBARI SVN Repository|CLT:Setting up SmartSVN]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository] {color:#ff0000}\- Non&nbsp;SVN client&nbsp;method{color}

[View the SVN Repository|http://kahuna.shore.mbari.org/viewvc/?root=svn]

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<property name="body"><![CDATA[h2.


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h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

{color:#ff0033}{*}NOTE:*{color} {color:#ff0033}In the rare event the administrator is on vacation or unavailable, please&nbsp;submit your CVS request to the IS Remedy page at:&nbsp;{color} [https://ishelp.shore.mbari.org/helpdesk/WebObjects/Helpdesk] {color:#ff0033}and it will be assigned by IS appropriately based on urgency level.{color}

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;CVS command Line Reference. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/.&nbsp];

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

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[Welcome to CVS\!|https://oceana.mbari.org/confluence/display/CLT/Welcome+to+CVS%21] \- {color:#ff0000}(New Users{color} {color:#ff0000}{*}{+}MUST{+}{*}{color} {color:#ff0000}Read and Provide Password for CVS Access\!){color}

[CVS Graphical User Interface (GUI) Client Software Downloads|CLT:CVS Client Software Downloads] \- {color:#3300cc}Windows, Mac, Linux Systems{color}

[Setting up&nbsp;the WinCVS GUI|https://oceana.mbari.org/confluence/display/CLT/Setting+up+CVS+Graphical+User+Interface+%28GUI%29]

[Adding code to CVS Repository with WinCVS GUI|CLT:Adding code to CVS Repository with WinCVS GUI]

[Command Line Access to CVS Repository&nbsp;(i.e., no GUI)|CLT:Setup to access CVS Repository with Command line instead of GUI (Linux users)] *\-* {color:#3300cc}For Linux System Users{color}

[View the CVS Repository|http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/ ]\\
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# ADCP: Acoustic Doppler Current Profiler - a sonar that attempts to produce a record of water current velocities for a range of depths [http://en.wikipedia.org/wiki/Acoustic_Doppler_Current_Profiler]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AMQP: Advanced Message Queuing Protocol - [http://www.amqp.org]
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ARI-WG: Access to Remote Instrumentation in a distributed environment - Working Group. OpenGrid Forum [http://www.ogf.org/gf/group_info/view.php?group=ari-wg]
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EarthCube: EarthCube is a NSF activity to create a data and knowledge management system for the 21st Century. The scientific objective is to develop a framework over the next decade to understand and predict the Earth system from the sun to the center of the Earth [http://earthcube.ning.com/]
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GNB: Gaussian Naïve Bayes. GNB is a probabilistic classifier relying on Bayes rule to estimate posterior probabilities of labels given the data. Naive assumption in it is an independence of the features. See http://en.wikipedia.org/wiki/Naive_bayes for more information. 
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# HDF: Hierarchical Data Format
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# JVM: Java Virtual Machine - [http://en.wikipedia.org/wiki/Jvm]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MB/CA Current: a MBARI project in 2011
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MODIS: Moderate Resolution Imaging Spectroradiometer is a key instrument aboard the Terra (EOS AM) and Aqua (EOS PM) satellites.
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# MVC: Model-View-Controller software pattern - http://en.wikipedia.org/wiki/Model%E2%80%93view%E2%80%93controller
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NODC: National Oceanographic Data Center - http://www.nodc.noaa.gov/
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# ODSS: Oceanographic Decision Support System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOI CI: Ocean Observatories Initiative CyberInfrastructure: [http://ci.oceanobservatories.org/] (Developers site: [http://ooici.net/])
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software).
# SCPI: Self Contained Plankton Imager, an MBARI project in 2011
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WCS: Web Coverage Service
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[h2.


----
h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.&nbsp;

To use SVN first requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org). {color:#ff0033}{*}NOTE:*{color} {color:#ff0033}In the rare event the administrator is on vacation or unavailable, please&nbsp;submit your&nbsp;SVN request to the IS Remedy page at:&nbsp;{color} [https://ishelp.shore.mbari.org/helpdesk/WebObjects/Helpdesk] {color:#ff0033}and it will be assigned by IS appropriately based on urgency level.{color}

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

\\
&nbsp;

[SVN Client Software Downloads|CLT:SVN Client Software Downloads] {color:#ff0000}\- Windows, Macs, Linux Systems{color}

[Setting up SVN Client&nbsp;to MBARI SVN Repository|CLT:Setting up SmartSVN]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository] {color:#ff0000}\- Non&nbsp;SVN client&nbsp;method{color}

[View the SVN Repository|http://kahuna.shore.mbari.org/cgi-bin/viewvc]\\
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# ADCP: Acoustic Doppler Current Profiler -- a sonar that attempts to produce a record of water current velocities for a range of depths [http://en.wikipedia.org/wiki/Acoustic_Doppler_Current_Profiler] 
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AMQP: Advanced Message Queuing Protocol - [http://www.amqp.org]
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ARI-WG: Access to Remote Instrumentation in a distributed environment - Working Group. OpenGrid Forum [http://www.ogf.org/gf/group_info/view.php?group=ari-wg]
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EarthCube: EarthCube is a NSF activity to create a data and knowledge management system for the 21st Century. The scientific objective is to develop a framework over the next decade to understand and predict the Earth system from the sun to the center of the Earth http://earthcube.ning.com/  
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# HDF: Hierarchical Data Format
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# JVM: Java Virtual Machine - http://en.wikipedia.org/wiki/Jvm
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MB/CA Current: a MBARI project in 2011
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# ODSS: Oceanographic Decision Support System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOI CI: Ocean Observatories Initiative CyberInfrastructure: [http://ci.oceanobservatories.org/] (Developers site: [http://ooici.net/])
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software).
# SCPI: Self Contained Plankton Imager, an MBARI project in 2011
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WCS: Web Coverage Service
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit their respective websites.

Contact Kevin Gomes [mailto:kgomes@mbari.org], Brian Schlining [mailto:brian@mbari.org] or Kent Headley [mailto:headley@mbari.org] with questions or permission requests for certain tools.

{tip:title=External Availability}
Please note that Confluence, JIRA, and Alfresco are all available outside the MBARI firewall and can have external collaborator accounts that are not MBARI accounts.  This was a desirable feature of these tools and allows us to externally collaborate without risking security breaches at MBARI.
{tip}

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.
----
h3. Authentication and Single Sign On With Crowd

[Crowd|http://www.atlassian.com/crowd] is an authentication tool that is developed by [Atlassian|http://www.atlassian.com] and is provided to MBARI under a community/non-profit license.  It provides an internal user database so we can create external user accounts that can then be linked to other applications such as JIRA and Confluence.  It also connects to our internal MBARI user database using LDAP so that MBARI users can have Single Sign on capability across multiple applications.

Links for Crowd at MBARI:
* [Crowd Web Application|http://oceana.mbari.org:8095/crowd]
* [Documentation of MBARI Crowd Installation|SPEPRJ:MBARI Crowd Installation]

----
h3. Content Management with [Alfresco|https://alfresco.mbari.org/alfresco]

Alfresco is a Content Management System (CMS) intended to replace the Project Library on Tornado as the repository for MBARI project documentation. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

{info:title=Accounting Creates Projects in Alfresco}
One of the main benefits of Alfresco is that it can interact with our accounting system in an automated fashion. Because of this, we have the accounting system currently creating project spaces and directory structures in Alfresco automatically.  This allows the accounting software to then export all accounting activity (PDFs of AMEX, PO's, etc.) to the Alfresco spaces automatically.
{info}

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password without using "shore\" in front) to see the project library materials. The *Projects* folder is the space that contains the content for projects at MBARI.

To create a short cut to the Projects folder (or any folder), enter that folder, then select "More Actions/View Details", then "Create Shortcut" (on the right side of the page).  This will create a shortcut that will be available in the "Shelf".  To view the shortcuts in your "Shelf", click on the down arrow next to "Navigtor" on the left hand sidebar menu, then select "Shelf" and you will see your created shortcuts.

Here are some useful links related to MBARI's installation of Alfresco:
* [Alfresco's Homepage|http://www.alfresco.com/]
* [Alfresco's Developer Home Page|http://wiki.alfresco.com/wiki/Main_Page]
* [Alfresco's Enterprise Customer Portal|https://network.alfresco.com/extranet/]
* [Deployment Information for MBARI's Alfresco Installation|Deployment Information]
* [Installation Notes]
* [alfresco.mbari.org Installation Notes]
* [alfresco-test.shore.mbari.org Installation Notes]

----
h3. WIKI Collaboration Pages ([Confluence|https://oceana.mbari.org/confluence])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

# [SPEPRJ:Confluence Installation Notes]

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts an externally accessable Maven repository at [https://oceana.mbari.org/maven2], an internal repository at [http://seaspray.shore.mbari.org:8082/archiva/repository/internal/] and a repository manager at [http://seaspray.shore.mbari.org:8082/archiva]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [SPEPRJ:Maven At MBARI] for more details.

h3. Modeling with UML (JBuilder 2008 R2)

You can download JBuilder 2008 R2 from here:

[Mac OS X|http://altd.embarcadero.com/download/jbuilder/JBuilder_2008R2/jbuilder2008r2.macosx.tar.gz]
[Linux|http://altd.embarcadero.com/download/jbuilder/JBuilder_2008R2/jbuilder2008r2.linux.tar.gz]
[Windows|http://altd.embarcadero.com/download/jbuilder/JBuilder_2008R2/jbuilder2008r2.win32.zip]

Once downloaded and installed, you need to copy the following [.slip|https://alfresco.mbari.org/alfresco/webdav/Engineering/Tools/Collaboration%20Tools/JBuilder/concurrent_48444.slip] file to the:

JBUILDER_HOME/license

directory.

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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There are&nbsp;two recommended CVS Clients to access the MBARI CVS Respository including:&nbsp;{color:#ff0000}{*}WinCVS{*}{color} and {color:#ff0000}{*}SmartCVS{*}{color}.&nbsp;&nbsp; Both clients work for all major operating systems including Windows, Macintosh, and Linux systems.&nbsp;The key bits of information to use when setting up either client are the following:
* {color:#0000cc}Your access method needs to be set to&nbsp;{color}{color:#0000cc}{*}pserver{*}{color}{color:#0000cc}&nbsp;(SmartCVS) or{color} {color:#0000cc}{*}passwd file on server{*}{color} {color:#0000cc}(WinCVS){color}
* {color:#0000cc}User&nbsp; (Your MBARI user/e-mail&nbsp;account, e.g.,{color} {color:#0000cc}{_}salamy{_}{color}{color:#0000cc}){color}
* {color:#0000cc}Repository Server (MBARI CVS Repository is hosted on{color} {color:#0000cc}{*}{_}moonjelly{_}{*}{color}{color:#0000cc}){color}
* {color:#0000cc}CVSROOT ({color}{color:#0000cc}{*}_/home/cvs{_}{*}{color}{color:#0000cc}){color}

Thus, the full CVSROOT path for user _salamy_ would be:&nbsp;&nbsp;&nbsp; salamy@moonjelly:/home/cvs&nbsp;

----
\\

h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Windows-7.1.1.zip|^smartcvs-win32-setup-nojre-7_1_1.zip|SmartCVS Windows version 7.1.1] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOSX-7.1.1.tar.gz|^smartcvs-generic-7_1_1.tar.gz|SmartCVS Macintosh Version 7.1.1] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartSVN-Linux-7.1.1.tar.gz|^smartcvs-generic-7_1_1.tar.gz|SmartSVN Linux Version 7.1.1] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}({color}{color:#0066cc}{*}NOTE:*{color}{color:#0066cc}&nbsp;Setup same for MacCVS and gCVS as well){color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS Getting-Started Tutorial|^smartcvs-tutorial.pdf] \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

\\
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit their respective websites.

Contact Kevin Gomes [mailto:kgomes@mbari.org], Brian Schlining [mailto:brian@mbari.org] or Kent Headley [mailto:headley@mbari.org] with questions or permission requests for certain tools.

{tip:title=External Availability}
Please note that Confluence, JIRA, and Alfresco are all available outside the MBARI firewall and can have external collaborator accounts that are not MBARI accounts.  This was a desirable feature of these tools and allows us to externally collaborate without risking security breaches at MBARI.
{tip}

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.
----
h3. Authentication and Single Sign On With Crowd

[Crowd|http://www.atlassian.com/crowd] is an authentication tool that is developed by [Atlassian|http://www.atlassian.com] and is provided to MBARI under a community/non-profit license.  It provides an internal user database so we can create external user accounts that can then be linked to other applications such as JIRA and Confluence.  It also connects to our internal MBARI user database using LDAP so that MBARI users can have Single Sign on capability across multiple applications.

Links for Crowd at MBARI:
* [Crowd Web Application|http://oceana.mbari.org:8095/crowd]
* [Documentation of MBARI Crowd Installation|SPEPRJ:MBARI Crowd Installation]

----
h3. Content Management with [Alfresco|https://alfresco.mbari.org/alfresco]

Alfresco is a Content Management System (CMS) intended to replace the Project Library on Tornado as the repository for MBARI project documentation. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

{info:title=Accounting Creates Projects in Alfresco}
One of the main benefits of Alfresco is that it can interact with our accounting system in an automated fashion. Because of this, we have the accounting system currently creating project spaces and directory structures in Alfresco automatically.  This allows the accounting software to then export all accounting activity (PDFs of AMEX, PO's, etc.) to the Alfresco spaces automatically.
{info}

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password without using "shore\" in front) to see the project library materials. The *Projects* folder is the space that contains the content for projects at MBARI.

To create a short cut to the Projects folder (or any folder), enter that folder, then select "More Actions/View Details", then "Create Shortcut" (on the right side of the page).  This will create a shortcut that will be available in the "Shelf".  To view the shortcuts in your "Shelf", click on the down arrow next to "Navigtor" on the left hand sidebar menu, then select "Shelf" and you will see your created shortcuts.

Here are some useful links related to MBARI's installation of Alfresco:
* [Alfresco's Homepage|http://www.alfresco.com/]
* [Alfresco's Developer Home Page|http://wiki.alfresco.com/wiki/Main_Page]
* [Alfresco's Enterprise Customer Portal|https://network.alfresco.com/extranet/]
* [Deployment Information for MBARI's Alfresco Installation|Deployment Information]
* [Installation Notes]
* [alfresco.mbari.org Installation Notes]
* [alfresco-test.shore.mbari.org Installation Notes]

----
h3. WIKI Collaboration Pages ([Confluence|https://oceana.mbari.org/confluence])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

# [SPEPRJ:Confluence Installation Notes]

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts an externally accessable Maven repository at [https://oceana.mbari.org/maven2], an internal repository at [http://seaspray.shore.mbari.org:8082/archiva/repository/internal/] and a repository manager at [http://seaspray.shore.mbari.org:8082/archiva]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modeling with UML (JBuilder 2008 R2)

You can download JBuilder 2008 R2 from here:

[http://embarcadero.com/downloads/index.php]

Once downloaded and installed, you need to copy the following [.slip|https://alfresco.mbari.org/alfresco/webdav/Engineering/Tools/Collaboration%20Tools/JBuilder/concurrent_48444.slip] file to the:

JBUILDER_HOME/license

directory.

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository http://mmisw.org/orr/
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10912128</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10944890</id>
<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit their respective websites.

Contact Kevin Gomes [mailto:kgomes@mbari.org], Brian Schlining [mailto:brian@mbari.org] or Kent Headley [mailto:headley@mbari.org] with questions or permission requests for certain tools.

{tip:title=External Availability}
Please note that Confluence, JIRA, and Alfresco are all available outside the MBARI firewall and can have external collaborator accounts that are not MBARI accounts.  This was a desirable feature of these tools and allows us to externally collaborate without risking security breaches at MBARI.
{tip}

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.
----
h3. Authentication and Single Sign On With Crowd

[Crowd|http://www.atlassian.com/crowd] is an authentication tool that is developed by [Atlassian|http://www.atlassian.com] and is provided to MBARI under a community/non-profit license.  It provides an internal user database so we can create external user accounts that can then be linked to other applications such as JIRA and Confluence.  It also connects to our internal MBARI user database using LDAP so that MBARI users can have Single Sign on capability across multiple applications.

Links for Crowd at MBARI:
* [Crowd Web Application|http://oceana.mbari.org:8095/crowd]
* [Documentation of MBARI Crowd Installation|SPEPRJ:MBARI Crowd Installation]

----
h3. Content Management with [Alfresco|https://alfresco.mbari.org/alfresco]

Alfresco is a Content Management System (CMS) intended to replace the Project Library on Tornado as the repository for MBARI project documentation. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

{info:title=Accounting Creates Projects in Alfresco}
One of the main benefits of Alfresco is that it can interact with our accounting system in an automated fashion. Because of this, we have the accounting system currently creating project spaces and directory structures in Alfresco automatically.  This allows the accounting software to then export all accounting activity (PDFs of AMEX, PO's, etc.) to the Alfresco spaces automatically.
{info}

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password without using "shore\" in front) to see the project library materials. The *Projects* folder is the space that contains the content for projects at MBARI.

To create a short cut to the Projects folder (or any folder), enter that folder, then select "More Actions/View Details", then "Create Shortcut" (on the right side of the page).  This will create a shortcut that will be available in the "Shelf".  To view the shortcuts in your "Shelf", click on the down arrow next to "Navigtor" on the left hand sidebar menu, then select "Shelf" and you will see your created shortcuts.

Here are some useful links related to MBARI's installation of Alfresco:
* [Alfresco's Homepage|http://www.alfresco.com/]
* [Alfresco's Developer Home Page|http://wiki.alfresco.com/wiki/Main_Page]
* [Alfresco's Enterprise Customer Portal|https://network.alfresco.com/extranet/]
* [Deployment Information for MBARI's Alfresco Installation|Deployment Information]
* [Installation Notes]
* [alfresco.mbari.org Installation Notes]
* [alfresco-test.shore.mbari.org Installation Notes]

----
h3. WIKI Collaboration Pages ([Confluence|https://oceana.mbari.org/confluence])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

# [SPEPRJ:Confluence Installation Notes]

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts an externally accessable Maven repository at [https://oceana.mbari.org/maven2], an internal repository at [http://seaspray.shore.mbari.org:8082/archiva/repository/internal/] and a repository manager at [http://seaspray.shore.mbari.org:8082/archiva]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [SPEPRJ:Maven At MBARI] for more details.

h3. Modeling with UML (JBuilder 2008 R2)

You can download JBuilder 2008 R2 from here:

[http://embarcadero.com/downloads/index.php]

Once downloaded and installed, you need to copy the following [.slip|https://alfresco.mbari.org/alfresco/webdav/Engineering/Tools/Collaboration%20Tools/JBuilder/concurrent_48444.slip] file to the:

JBUILDER_HOME/license

directory.

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit their respective websites.

Contact Kevin Gomes [mailto:kgomes@mbari.org], Brian Schlining [mailto:brian@mbari.org] or Kent Headley [mailto:headley@mbari.org] with questions or permission requests for certain tools.

{tip:title=External Availability}
Please note that Confluence, JIRA, and Alfresco are all available outside the MBARI firewall and can have external collaborator accounts that are not MBARI accounts.  This was a desirable feature of these tools and allows us to externally collaborate without risking security breaches at MBARI.
{tip}

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.
----
h3. Authentication and Single Sign On With Crowd

[Crowd|http://www.atlassian.com/crowd] is an authentication tool that is developed by [Atlassian|http://www.atlassian.com] and is provided to MBARI under a community/non-profit license.  It provides an internal user database so we can create external user accounts that can then be linked to other applications such as JIRA and Confluence.  It also connects to our internal MBARI user database using LDAP so that MBARI users can have Single Sign on capability across multiple applications.

Links for Crowd at MBARI:
* [MBARI Crowd Installation]

----
h3. Content Management with [Alfresco|https://alfresco.mbari.org/alfresco]

Alfresco is a Content Management System (CMS) intended to replace the Project Library on Tornado as the repository for MBARI project documentation. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

{info:title=Accounting Creates Projects in Alfresco}
One of the main benefits of Alfresco is that it can interact with our accounting system in an automated fashion. Because of this, we have the accounting system currently creating project spaces and directory structures in Alfresco automatically.  This allows the accounting software to then export all accounting activity (PDFs of AMEX, PO's, etc.) to the Alfresco spaces automatically.
{info}

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password without using "shore\" in front) to see the project library materials. The *Projects* folder is the space that contains the content for projects at MBARI.

To create a short cut to the Projects folder (or any folder), enter that folder, then select "More Actions/View Details", then "Create Shortcut" (on the right side of the page).  This will create a shortcut that will be available in the "Shelf".  To view the shortcuts in your "Shelf", click on the down arrow next to "Navigtor" on the left hand sidebar menu, then select "Shelf" and you will see your created shortcuts.

Here are some useful links related to MBARI's installation of Alfresco:
* [Alfresco's Homepage|http://www.alfresco.com/]
* [Alfresco's Developer Home Page|http://wiki.alfresco.com/wiki/Main_Page]
* [Alfresco's Enterprise Customer Portal|https://network.alfresco.com/extranet/]
* [Deployment Information for MBARI's Alfresco Installation|Deployment Information]
* [Installation Notes]
* [alfresco.mbari.org Installation Notes]
* [alfresco-test.shore.mbari.org Installation Notes]

----
h3. WIKI Collaboration Pages ([Confluence|http://oceana.shore.mbari.org:8081/dashboard.action])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts an externally accessable Maven repository at [https://oceana.mbari.org/maven2], an internal repository at [http://seaspray.shore.mbari.org:8082/archiva/repository/internal/] and a repository manager at [http://seaspray.shore.mbari.org:8082/archiva]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modeling with UML (JBuilder 2008 Enterprise)

You can download JBuilder 2008 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded and installed, you need to copy the following [.slip|https://alfresco.mbari.org/alfresco/webdav/Engineering/Tools/Collaboration%20Tools/CodeGear%20JBuilder/concurrent_31474.slip] file to the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software Integration).&nbsp;
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">15204472</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">10944817</id>
<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. http://www.redhat.com/mrg/&nbsp;
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">10912058</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">9830546</id>
<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - http://www.oostethys.org/ogc-oceans-interoperability-experiment
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MB/CA Current: a MBARI project in 2011
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOI CI: Ocean Observatories Initiative CyberInfrastructure: [http://ci.oceanobservatories.org/] (Developers site: [http://ooici.net/])
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software).
# SCPI: Self Contained Plankton Imager, an MBARI project in 2011
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - http://www.oostethys.org/ogc-oceans-interoperability-experiment
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOR: Open Ontology Repository initiative - http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[\\

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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

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h3. *SmartSVN GUI Installation Files*


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h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.3.zip|^smartsvn-win32-setup-nojre-4_0_3.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]
* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|^SmartSVN.zip]
\\

\\

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h3. Macintosh

{color:#000000}({color}{color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color}{color:#000000}){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

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h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to /opt/alfresco.2.0/tomcat/webapps/alfresco/images/logo and overwrite the one that is there.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
{noformat}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
## Now edit /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
      
   </security-constraint>
{noformat}
# TODO: Setup backup for MySQL database
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

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h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* {color:#ff0000}[{color:#ff0000}SmartSVN-4.0.3.zip{color}|^smartsvn-win32-setup-nojre-4_0_3.zip]{color}
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]
* [SmartSVN-3.0.7.zip|^smartsvn-win32-setup-nojre-3_0_7.zip]
* [SmartSVN-3.0.4.zip|^SmartSVN.zip]
\\

\\

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h3. Macintosh

{color:#000000}({color}{color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color}{color:#000000}){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
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h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - http://code.google.com/webtoolkit/
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to /opt/alfresco.2.0/tomcat/webapps/alfresco/images/logo and overwrite the one that is there.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
{noformat}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Now, it is time to setup the server so we can login over SSL.]]></property>
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* {color:#000000}[{color:#000000}SmartSVN-3.0.9.zip{color}|^smartsvn-win32-setup-nojre-3_0_9.zip]{color}\\ \\
\\
\---\-
h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color}{color:#000000}){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
\\
\\]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODV: Ocean Data View [http://www.oceansites.org/]
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - http://www.ietf.org/rfc/rfc2396.txt
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to /opt/alfresco.2.0/tomcat/webapps/alfresco/images/logo and overwrite the one that is there.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
{noformat}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
## Now edit /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
      
   </security-constraint>
{noformat}]]></property>
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<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* {color:#000000}[{color:#000000}SmartSVN-3.0.9.zip{color}|^smartsvn-win32-setup-nojre-3_0_9.zip]{color}\\

----
h3. Macintosh



(Note: all require Mac&nbsp;OS X, version 10.4 or higher{color:#000000}){color}
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
\\
\\]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
 {noformat}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}]]></property>
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<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* {color:#000000}\[{color}{color:#000000}SmartSVN-3.0.9.zip{color}\|^smartsvn-win32-setup-nojre-3_0_9.zip\]\\ \\

----
h3. Macintosh



(Note: all require Mac&nbsp;OS X, version 10.4 or higher)

* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
\\
\\]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to /opt/alfresco.2.0/tomcat/webapps/alfresco/images/logo and overwrite the one that is there.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
{noformat}

{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}]]></property>
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<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* {color:#000000}SmartSVN-3.0.9.zip{color}\\

----
h3. Macintosh

(Note: all require Mac&nbsp;OS X, version 10.4 or higher)
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
\\
\\]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
 {noformat}]]></property>
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<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* {color:#000000}SmartSVN-3.0.9.zip{color}\\

----
h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
\\
\\]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
 {noformat}]]></property>
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<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* {color:#000000}SmartSVN-3.0.9.zip{color}\\ \\

----
h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
\\
\\]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
 {noformat}]]></property>
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<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* {color:#000000}SmartSVN-3.0.9.zip{color}\\

\\

----
h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
\\
\\]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
 {noformat}]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to tweak the web client ui a bit as well.  I cd'd to /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages.  I then edited the webclient.properties file.
## Changed company_home from 'Company Home' to 'MBARI'
{note}
Although this is supposed to work, it does not appear to have any affect
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
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<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* {color:#000000}[{color:#000000}SmartSVN-3.0.9.zip{color}|^smartsvn-win32-setup-nojre-3_0_9.zip]{color}\\

\\

----
h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
\\
\\]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to tweak the web client ui a bit as well.  I cd'd to /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages.  I then edited the webclient.properties file.
## Changed company_home from 'Company Home' to 'MBARI'
{note}
Although this is supposed to work, it does not appear to have any affect
{note}
# Since that did not seem to change the company home, I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two line to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
## Now edit /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
      
   </security-constraint>
{noformat}
# Next, I needed to configure the CIFS server
## I edited the file /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/file-servers.xml
### I added 'domain="SHORE' to the <host ...> tag.
### I made sure the domain broadcast submask was 255.255.254.0
### I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
### I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# TODO: Integrate with OpenOffice
# Setup backup
## On the server, mysql 5 was already installed as a service (whoo-hoo!).
## The first thing to do is to turn on binary logging.  This is done when the mysql service is started.  On oceana, the startup script is /etc/init.d/mysql.  I vi'd the script and added the binary log option to the actual startup command.  So I changed:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" >/dev/null 2>&1 &
{noformat}
to:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" --log-bin=/data/mysql_logs/oceana-bin --log-bin-index=/data/mysql_logs/oceana-bin-idx >/dev/null 2>&1 &
{noformat}
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to /opt/alfresco.2.0/tomcat/webapps/alfresco/images/logo and overwrite the one that is there.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
## Now edit /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
      
   </security-constraint>
{noformat}
# Next, I needed to configure the CIFS server
## I edited the file /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/file-servers.xml
### I added 'domain="SHORE' to the <host ...> tag.
### I made sure the domain broadcast submask was 255.255.254.0
### I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
### I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# TODO: Integrate with OpenOffice
# Setup backup
## On the server, mysql 5 was already installed as a service (whoo-hoo!).
## The first thing to do is to turn on binary logging.  This is done when the mysql service is started.  On oceana, the startup script is /etc/init.d/mysql.  I vi'd the script and added the binary log option to the actual startup command.  So I changed:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" >/dev/null 2>&1 &
{noformat}
to:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" --log-bin=/data/mysql_logs/oceana-bin --log-bin-index=/data/mysql_logs/oceana-bin-idx >/dev/null 2>&1 &
{noformat}
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to /opt/alfresco.2.0/tomcat/webapps/alfresco/images/logo and overwrite the one that is there.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
## Now edit /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
      
   </security-constraint>
{noformat}
# Next, I needed to configure the CIFS server
## I edited the file /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/file-servers.xml
### I added 'domain="SHORE' to the <host ...> tag.
### I made sure the domain broadcast submask was 255.255.254.0
### I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
### I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# TODO: Integrate with OpenOffice
# Setup backup
## On the server, mysql 5 was already installed as a service (whoo-hoo!).
## The first thing to do is to turn on binary logging.  This is done when the mysql service is started.  On oceana, the startup script is /etc/init.d/mysql.  I vi'd the script and added the binary log option to the actual startup command.  So I changed:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" >/dev/null 2>&1 &
{noformat}
to:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" --log-bin=/data/mysql_logs/oceana-bin --log-bin-index=/data/mysql_logs/oceana-bin-idx >/dev/null 2>&1 &
{noformat}
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to /opt/alfresco.2.0/tomcat/webapps/alfresco/images/logo and overwrite the one that is there.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
## Now edit /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
      
   </security-constraint>
{noformat}
# Next, I needed to configure the CIFS server
## I edited the file /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/file-servers.xml
### I added 'domain="SHORE' to the <host ...> tag.
### I made sure the domain broadcast submask was 255.255.254.0
### I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
### I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# TODO: Integrate with OpenOffice
# Setup backup
## On the server, mysql 5 was already installed as a service (whoo-hoo!).
## The first thing to do is to turn on binary logging.  This is done when the mysql service is started.  On oceana, the startup script is /etc/init.d/mysql.  I vi'd the script and added the binary log option to the actual startup command.  So I changed:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" >/dev/null 2>&1 &
{noformat}
to:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" --log-bin=/data/mysql_logs/oceana-bin --log-bin-index=/data/mysql_logs/oceana-bin-idx >/dev/null 2>&1 &
{noformat}
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64.  To fix, I created symbolic links for those in /usr/lib using:
### cd /usr/lib
### ln -sf /usr/lib64/libgnome-2* .
### ln -sf /usr/lib64/libgconf-2* .
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to /opt/alfresco.2.0/tomcat/webapps/alfresco/images/logo and overwrite the one that is there.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
## Now edit /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
      
   </security-constraint>
{noformat}
# Next, I needed to configure the CIFS server
## I edited the file /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/file-servers.xml
### I added 'domain="SHORE' to the <host ...> tag.
### I made sure the domain broadcast submask was 255.255.254.0
### I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
### I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# TODO: Integrate with OpenOffice
# Setup backup
## On the server, mysql 5 was already installed as a service (whoo-hoo!).
## The first thing to do is to turn on binary logging.  This is done when the mysql service is started.  On oceana, the startup script is /etc/init.d/mysql.  I vi'd the script and added the binary log option to the actual startup command.  So I changed:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" >/dev/null 2>&1 &
{noformat}
to:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" --log-bin=/data/mysql_logs/oceana-bin --log-bin-index=/data/mysql_logs/oceana-bin-idx >/dev/null 2>&1 &
{noformat}
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## I was missing two dependencies (libgnomevfs and libgconf).

# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to /opt/alfresco.2.0/tomcat/webapps/alfresco/images/logo and overwrite the one that is there.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
## Now edit /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
      
   </security-constraint>
{noformat}
# Next, I needed to configure the CIFS server
## I edited the file /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/file-servers.xml
### I added 'domain="SHORE' to the <host ...> tag.
### I made sure the domain broadcast submask was 255.255.254.0
### I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
### I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# TODO: Integrate with OpenOffice
# Setup backup
## On the server, mysql 5 was already installed as a service (whoo-hoo!).
## The first thing to do is to turn on binary logging.  This is done when the mysql service is started.  On oceana, the startup script is /etc/init.d/mysql.  I vi'd the script and added the binary log option to the actual startup command.  So I changed:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" >/dev/null 2>&1 &
{noformat}
to:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" --log-bin=/data/mysql_logs/oceana-bin --log-bin-index=/data/mysql_logs/oceana-bin-idx >/dev/null 2>&1 &
{noformat}
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to /opt/alfresco.2.0/tomcat/webapps/alfresco/images/logo and overwrite the one that is there.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
## Now edit /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
      
   </security-constraint>
{noformat}
# Next, I needed to configure the CIFS server
## I edited the file /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/file-servers.xml
### I added 'domain="SHORE' to the <host ...> tag.
### I made sure the domain broadcast submask was 255.255.254.0
### I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
### I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# TODO: Integrate with OpenOffice
# Setup backup
## On the server, mysql 5 was already installed as a service (whoo-hoo!).
## The first thing to do is to turn on binary logging.  This is done when the mysql service is started.  On oceana, the startup script is /etc/init.d/mysql.  I vi'd the script and added the binary log option to the actual startup command.  So I changed:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" >/dev/null 2>&1 &
{noformat}
to:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" --log-bin=/data/mysql_logs/oceana-bin --log-bin-index=/data/mysql_logs/oceana-bin-idx >/dev/null 2>&1 &
{noformat}
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# ADCP: Acoustic Doppler Current Profiler - a sonar that attempts to produce a record of water current velocities for a range of depths [http://en.wikipedia.org/wiki/Acoustic_Doppler_Current_Profiler]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AMQP: Advanced Message Queuing Protocol - [http://www.amqp.org]
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ARI-WG: Access to Remote Instrumentation in a distributed environment - Working Group. OpenGrid Forum [http://www.ogf.org/gf/group_info/view.php?group=ari-wg]
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CGSN: Coastal & Global Scale Nodes - [http://www.whoi.edu/ooi_cgsn/home]
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EarthCube: EarthCube is a NSF activity to create a data and knowledge management system for the 21st Century. The scientific objective is to develop a framework over the next decade to understand and predict the Earth system from the sun to the center of the Earth [http://earthcube.ning.com/]
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GNB: Gaussian Naïve Bayes. GNB is a probabilistic classifier relying on Bayes rule to estimate posterior probabilities of labels given the data. Naive assumption in it is an independence of the features. See [http://en.wikipedia.org/wiki/Naive_bayes] for more information.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# HDF: Hierarchical Data Format
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# JVM: Java Virtual Machine - [http://en.wikipedia.org/wiki/Jvm]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MB/CA Current: a MBARI project in 2011
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MODIS: Moderate Resolution Imaging Spectroradiometer is a key instrument aboard the Terra (EOS AM) and Aqua (EOS PM) satellites.
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# MVC: Model-View-Controller software pattern - [http://en.wikipedia.org/wiki/Model%E2%80%93view%E2%80%93controller]
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NODC: National Oceanographic Data Center - [http://www.nodc.noaa.gov/]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# ODSS: Oceanographic Decision Support System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOI CI: Ocean Observatories Initiative CyberInfrastructure: [http://ci.oceanobservatories.org/] (Developers site: [http://ooici.net/])
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software).
# SCPI: Self Contained Plankton Imager, an MBARI project in 2011
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WCS: Web Coverage Service
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to /opt/alfresco.2.0/tomcat/webapps/alfresco/images/logo and overwrite the one that is there.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
## Now edit /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
      
   </security-constraint>
{noformat}
# Next, I needed to configure the CIFS server
## I edited the file /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/file-servers.xml
### I added 'domain="SHORE' to the <host ...> tag.
### I made sure the domain broadcast submask was 255.255.254.0
### I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
### I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# TODO: Integrate with OpenOffice
# Setup backup
## On the server, mysql 5 was already installed as a service (whoo-hoo!).
## The first thing to do is to turn on binary logging.  This is done when the mysql service is started.  On oceana, the startup script is /etc/init.d/mysql.  I vi'd the script and added the binary log option to the actual startup command.  So I changed:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" >/dev/null 2>&1 &
{noformat}
to:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" --log-bin=/data/mysql_logs/oceana-bin --log-bin-index=/data/mysql_logs/oceana-bin-idx >/dev/null 2>&1 &
{noformat}
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to /opt/alfresco.2.0/tomcat/webapps/alfresco/images/logo and overwrite the one that is there.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
## Now edit /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
      
   </security-constraint>
{noformat}
# Next, I needed to configure the CIFS server
## I edited the file /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/file-servers.xml
### I added 'domain="SHORE' to the <host ...> tag.
### I made sure the domain broadcast submask was 255.255.254.0
### I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
### I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# TODO: Integrate with OpenOffice
# TODO: Setup backup for MySQL database
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to /opt/alfresco.2.0/tomcat/webapps/alfresco/images/logo and overwrite the one that is there.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
{noformat}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
## Now edit /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
      
   </security-constraint>
{noformat}
# Next, I needed to configure the CIFS server
## I edited the file /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/file-servers.xml
### I added 'domain="SHORE' to the <host ...> tag.
### I made sure the domain broadcast submask was 255.255.254.0
### I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
# TODO: Integrate with OpenOffice
# TODO: Setup backup for MySQL database
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to /opt/alfresco.2.0/tomcat/webapps/alfresco/images/logo and overwrite the one that is there.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
{noformat}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
## Now edit /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
      
   </security-constraint>
{noformat}
# Next, I needed to configure the CIFS server
## I edited the file /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/file-servers.xml
### I added 'domain="SHORE' to the <host ...> tag.
### I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
# TODO: Integrate with OpenOffice
# TODO: Setup backup for MySQL database
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[h2. Introduction

This space contains information about the collaboration and design tools that we use at MBARI. The links below will take you to the MBARI installation of each tool. For a more detailed description of the tools themselves, visit their respective websites.

Contact Kevin Gomes [mailto:kgomes@mbari.org], Brian Schlining [mailto:brian@mbari.org] or Kent Headley [mailto:headley@mbari.org] with questions or permission requests for certain tools.

{tip:title=External Availability}
Please note that Confluence, JIRA, and Alfresco are all available outside the MBARI firewall and can have external collaborator accounts that are not MBARI accounts.  This was a desirable feature of these tools and allows us to externally collaborate without risking security breaches at MBARI.
{tip}

h2. Best Practices

When creating 'spaces' (collaborative areas) in the collaborative development environments, we ask users to start the project name with the MBARI project number, if there is one. Follow the templates of the other projects. (Note that an MBARI project number is _not_ required in order to add a space to these environments.)

We encourage users to store most content, and *all* documentation related to MBARI engineering projects, in the Alfresco environment. Its content management features are extensive, and its content will be much more readily accessible within MBARI than the content in other spaces. Confluence is particularly appropriate to make multiple discussions and pages (text or HTML) accessible and editable by MBARI staff, especially for informal content.
----
h3. Authentication and Single Sign On With Crowd

[Crowd|http://www.atlassian.com/crowd] is an authentication tool that is developed by [Atlassian|http://www.atlassian.com] and is provided to MBARI under a community/non-profit license.  It provides an internal user database so we can create external user accounts that can then be linked to other applications such as JIRA and Confluence.  It also connects to our internal MBARI user database using LDAP so that MBARI users can have Single Sign on capability across multiple applications.

Links for Crowd at MBARI:
* [Crowd Web Application|http://oceana.mbari.org:8095/crowd]
* [Documentation of MBARI Crowd Installation|MBARI Crowd Installation]

----
h3. Content Management with [Alfresco|https://alfresco.mbari.org/alfresco]

Alfresco is a Content Management System (CMS) intended to replace the Project Library on Tornado as the repository for MBARI project documentation. New projects are typically created on Alfresco rather than the Project Library share, and old projects are migrated as their owners see fit.

{info:title=Accounting Creates Projects in Alfresco}
One of the main benefits of Alfresco is that it can interact with our accounting system in an automated fashion. Because of this, we have the accounting system currently creating project spaces and directory structures in Alfresco automatically.  This allows the accounting software to then export all accounting activity (PDFs of AMEX, PO's, etc.) to the Alfresco spaces automatically.
{info}

Your first visit you may see the Guest page. You must log in to Alfresco (MBARI network login/password without using "shore\" in front) to see the project library materials. The *Projects* folder is the space that contains the content for projects at MBARI.

To create a short cut to the Projects folder (or any folder), enter that folder, then select "More Actions/View Details", then "Create Shortcut" (on the right side of the page).  This will create a shortcut that will be available in the "Shelf".  To view the shortcuts in your "Shelf", click on the down arrow next to "Navigtor" on the left hand sidebar menu, then select "Shelf" and you will see your created shortcuts.

Here are some useful links related to MBARI's installation of Alfresco:
* [Alfresco's Homepage|http://www.alfresco.com/]
* [Alfresco's Developer Home Page|http://wiki.alfresco.com/wiki/Main_Page]
* [Alfresco's Enterprise Customer Portal|https://network.alfresco.com/extranet/]
* [Deployment Information for MBARI's Alfresco Installation|Deployment Information]
* [Installation Notes]
* [alfresco.mbari.org Installation Notes]
* [alfresco-test.shore.mbari.org Installation Notes]

----
h3. WIKI Collaboration Pages ([Confluence|https://oceana.mbari.org/confluence])

Confluence provides an environment to collaboratively work on activities and projects. Log in with your network account.

Navigation starts from the Dashboard, the page you see on entry. Use the blue navigation bar at the top to get back to Dashboard. Some material is only visible if you are logged in, or if you have specific permission to view it.

Creating a 'team' in Confluence lets you organize a set of spaces to appear for that team.

Contact Kevin Gomes to create a new space or team in Confluence.

# [Confluence Installation Notes]

h3. Issue (bug) tracking ([JIRA|http://oceana.shore.mbari.org:8082/])

JIRA is a sophisticated bug tracking tool with advanced search features. It is also well suited to tracking tasks and feature requests for a project.

JIRA has a small number of projects tracking bugs and issues on it now, but is being considered as a replacement for phpbt, the engineering bug tracking database.

Log in with your network account. You may find the Browse Projects tab (in the blue task bar at the top) a more convenient way to see the projects in JIRA.

Contact Kevin Gomes to create a new JIRA project.

h3. Maven Dependency Repository [Maven|http://oceana.shore.mbari.org/maven2]

MBARI hosts an externally accessable Maven repository at [https://oceana.mbari.org/maven2], an internal repository at [http://seaspray.shore.mbari.org:8082/archiva/repository/internal/] and a repository manager at [http://seaspray.shore.mbari.org:8082/archiva]. [Maven|http://maven.apache.org/] is a software project management and comprehension tool. Similar to [Ant|http://ant.apache.org/], Maven offers powerful dependency management features. The core of dependency management is the _Maven repository_ where builds of Java code can be shared with others and easily included in projects. By using repository aware build tools, such as [Maven|http://maven.apache.org/] or Ant (via [Ivy|http://incubator.apache.org/ivy/]), projects can be built without requiring the developer to check in all the dependencies in local version control. Instead, the dependencies are fetched from the repository by the build tools when they are needed.

See [Maven At MBARI] for more details.

h3. Modeling with UML (JBuilder 2008 Enterprise)

You can download JBuilder 2008 Enterprise from here:

[http://cc.codegear.com/free/jbuilder]

Once downloaded and installed, you need to copy the following [.slip|https://alfresco.mbari.org/alfresco/webdav/Engineering/Tools/Collaboration%20Tools/CodeGear%20JBuilder/concurrent_31474.slip] file to the:

JBUILDER_HOME/jbuilder/eclipse/license

directory. {note:title=Together has been Deprecated}
As of September 25, 2007, we have moved to JBuilder 2007 (see notes above). You can still use Together, but we are not eligible for upgrade/patches. {note}

h3. Concurrent Versioning System

CVS&nbsp;(Concurrent Versioning System) is an open source software&nbsp;tool used by software&nbsp;developers to&nbsp;manage code&nbsp;changes within their source code tree.&nbsp; This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access&nbsp;when editing&nbsp;MBARI project files.&nbsp; Similar to Subversion, CVS enables programmers to store current and all previous records of code changes (along with those who made the changes) over the existense of the code.&nbsp; Access to projects on the CVS respository at MBARI, however, also requires a pre-set individual passwords for all users in order to make changes to the code.&nbsp; Without access permission, users may only view and download code - not upload it into the repository to make changes.&nbsp; Access is given to users who are part of that project's group on CVS.&nbsp; To gain a password or access to edit a project requires notification to the server administrator:&nbsp; Karen Salamy (salamy@mbari.org).

In addition to acquiring a password from the server administrator, you must also install a CVS software client.&nbsp; There are multiple CVS clients for most major operating systems including WinCVS (Windows), MacCVS (Macs), and gcvs (Linux).&nbsp;&nbsp;The CVS repository may also be accessed using the command line&nbsp;with the following syntax&nbsp;[CVS command Line Reference|^CVS-commandline-reference.pdf]. The most common CVS client at MBARI is WinCVS (version 1.2) which is a stable Windows version release.&nbsp;Additional information on these clients can be found at [http://cvsgui.sourceforge.net/.&nbsp]; Detailed documentation on using CVS can be found at [http://ximbiot.com/cvs/manual/].&nbsp;

The MBARI&nbsp;CVS repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/].

See [CVS at MBARI|CLT:CVS at MBARI]&nbsp;for more details.
\\
&nbsp;

h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

See [SVN at MBARI] for more details.
\\
&nbsp;

h3. Java Security Certificate

If you intend to distribute java applications via Java Web Start, you will need to _sign_ your jar files. Details about how to do this can be found at [Java Signing at MBARI]]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to /opt/alfresco.2.0/tomcat/webapps/alfresco/images/logo and overwrite the one that is there.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
{noformat}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
## Now edit /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
      
   </security-constraint>
{noformat}
# Next, I needed to configure the CIFS server
## I edited the file /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/file-servers.xml
### I added 'domain="SHORE' to the <host ...> tag.
### I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
# TODO: Integrate with OpenOffice
# TODO: Setup backup for MySQL database
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to /opt/alfresco.2.0/tomcat/webapps/alfresco/images/logo and overwrite the one that is there.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
{noformat}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
## Now edit /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
      
   </security-constraint>
{noformat}
# Next, I needed to configure the CIFS server
## I edited the file /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/file-servers.xml
### I added 'domain="SHORE' to the <host ...> tag.
### I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
# TODO: Setup backup for MySQL database
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]

\\
&nbsp;

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.9.tar.gz|^smartsvn-macosx-4_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.9.tar.gz|^smartsvn-generic-4_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]\\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.9.tar.gz|^smartsvn-macosx-4_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.9.tar.gz|^smartsvn-generic-4_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]\\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.9.tar.gz|smartsvn-macosx-4_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.9.tar.gz|^smartsvn-generic-4_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]\\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.9.tar.gz|^smartsvn-macosx-4_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.9.tar.gz|^smartsvn-generic-4_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# ADCP: Acoustic Doppler Current Profiler - a sonar that attempts to produce a record of water current velocities for a range of depths [http://en.wikipedia.org/wiki/Acoustic_Doppler_Current_Profiler]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AMQP: Advanced Message Queuing Protocol - [http://www.amqp.org]
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ARI-WG: Access to Remote Instrumentation in a distributed environment - Working Group. OpenGrid Forum [http://www.ogf.org/gf/group_info/view.php?group=ari-wg]
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CGSN: Coastal & Global Scale Nodes - [http://www.whoi.edu/ooi_cgsn/home]
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EarthCube: EarthCube is a NSF activity to create a data and knowledge management system for the 21st Century. The scientific objective is to develop a framework over the next decade to understand and predict the Earth system from the sun to the center of the Earth [http://earthcube.ning.com/]
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GNB: Gaussian Naïve Bayes. GNB is a probabilistic classifier relying on Bayes rule to estimate posterior probabilities of labels given the data. Naive assumption in it is an independence of the features. See [http://en.wikipedia.org/wiki/Naive_bayes] for more information.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GRIIDC: Gulf of Mexico Research Initiative Information and Data Cooperative [https://data.gulfresearchinitiative.org/about]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# HDF: Hierarchical Data Format
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# JVM: Java Virtual Machine - [http://en.wikipedia.org/wiki/Jvm]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MB/CA Current: a MBARI project in 2011
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MODIS: Moderate Resolution Imaging Spectroradiometer is a key instrument aboard the Terra (EOS AM) and Aqua (EOS PM) satellites.
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# MVC: Model-View-Controller software pattern - [http://en.wikipedia.org/wiki/Model%E2%80%93view%E2%80%93controller]
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NODC: National Oceanographic Data Center - [http://www.nodc.noaa.gov/]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTP: Network Time Protocol - a protocol to synchronize the clocks of computers over a network. [http://www.ntp.org/]
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# ODSS: Oceanographic Decision Support System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOI CI: Ocean Observatories Initiative CyberInfrastructure: [http://ci.oceanobservatories.org/] (Developers site: [http://ooici.net/])
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software).
# SCPI: Self Contained Plankton Imager, an MBARI project in 2011
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TRN: Terrain-Relative Navigation. Using sensors that can "read" nearby terrain and comparing that with a known map of the area to determine where you are.
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WCS: Web Coverage Service
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[h2.


----
h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

\\
&nbsp;

[SVN Client Software Downloads|CLT:SVN Client Software Downloads] {color:#ff0000}\- Windows, Macs, Linux Systems{color}

[Setting up SVN Client&nbsp;to MBARI SVN Repository|CLT:Setting up SmartSVN]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository] {color:#ff0000}\- Non&nbsp;SVN client&nbsp;method{color}

[View the SVN Repository|http://kahuna.shore.mbari.org/viewvc/?root=svn]

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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}]]></property>
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
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h3. *SmartSVN GUI Installation Files*


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h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]\\ \\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.9.tar.gz|^smartsvn-macosx-4_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
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----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.9.tar.gz|^smartsvn-generic-4_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line]]></property>
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<property name="body"><![CDATA[h3.


----
h3. Download and Install Client&nbsp;

To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
To set up the SmartSVN client, run the application.&nbsp; Next, choose "*Project"* from the&nbsp;Main Menu and then click on "*Check Out..."*

This should bring you to the following page:

\\ !Screen_Save_Checkout_small.jpg|align=left!\\
\\
\\

Click on the&nbsp;*"Manage"* button, create&nbsp;and edit a new profile called&nbsp;*"MBARI_SVN"*&nbsp;as follows:

\\ !Screen_Saver_Edit_Repo_small.jpg|align=left!\\
\\ {color:#ff0000}{*}NOTE\!\!&nbsp;*{color} Make sure you use your own personal *Login Name* when creating this profile and check that the *"Verify connection when pressing 'OK'"* box is clicked in order to verify that your computer is able to connect with the SVN server kahuna.
\\
\\
\\
Once you have&nbsp;properly set up your Profile Name, when you click&nbsp;*"Project"* and *"Check&nbsp;Out..."* from the&nbsp;Main Menu, you should see a&nbsp;a page to login to your account on the repository.&nbsp; Use your standard MBARI network account to log in.&nbsp; Once you have logged in successfully, you will see a list of all projects&nbsp;on&nbsp;the&nbsp;MBARI SVN&nbsp;Repository.\\

\\
&nbsp;]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}]]></property>
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<property name="body"><![CDATA[h2.


----
h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

\\
&nbsp;

[SVN Client Software Downloads|CLT:SVN Client Software Downloads] {color:#ff0000}\- Windows, Macs, Linux Systems{color}

[Setting up SVN Client&nbsp;to MBARI SVN Repository|CLT:Setting up SmartSVN]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository] {color:#ff0000}\- Non&nbsp;SVN client&nbsp;method{color}

[View the SVN Repository|http://kahuna.shore.mbari.org/viewvc/?root=svn]

\\
\\
\\
\\
&nbsp;
\\
\\
\\
\\]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# ADCP: Acoustic Doppler Current Profiler - a sonar that attempts to produce a record of water current velocities for a range of depths [http://en.wikipedia.org/wiki/Acoustic_Doppler_Current_Profiler]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AMQP: Advanced Message Queuing Protocol - [http://www.amqp.org]
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ARI-WG: Access to Remote Instrumentation in a distributed environment - Working Group. OpenGrid Forum [http://www.ogf.org/gf/group_info/view.php?group=ari-wg]
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CGSN: Coastal & Global Scale Nodes - [http://www.whoi.edu/ooi_cgsn/home]
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EarthCube: EarthCube is a NSF activity to create a data and knowledge management system for the 21st Century. The scientific objective is to develop a framework over the next decade to understand and predict the Earth system from the sun to the center of the Earth [http://earthcube.ning.com/]
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GNB: Gaussian Naïve Bayes. GNB is a probabilistic classifier relying on Bayes rule to estimate posterior probabilities of labels given the data. Naive assumption in it is an independence of the features. See [http://en.wikipedia.org/wiki/Naive_bayes] for more information.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# HDF: Hierarchical Data Format
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# JVM: Java Virtual Machine - [http://en.wikipedia.org/wiki/Jvm]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MB/CA Current: a MBARI project in 2011
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MODIS: Moderate Resolution Imaging Spectroradiometer is a key instrument aboard the Terra (EOS AM) and Aqua (EOS PM) satellites.
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# MVC: Model-View-Controller software pattern - [http://en.wikipedia.org/wiki/Model%E2%80%93view%E2%80%93controller]
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NODC: National Oceanographic Data Center - [http://www.nodc.noaa.gov/]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# ODSS: Oceanographic Decision Support System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOI CI: Ocean Observatories Initiative CyberInfrastructure: [http://ci.oceanobservatories.org/] (Developers site: [http://ooici.net/])
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software).
# SCPI: Self Contained Plankton Imager, an MBARI project in 2011
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TRN: Terrain-Relative Navigation. Using sensors that can "read" nearby terrain and comparing that with a known map of the area to determine where you are.
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WCS: Web Coverage Service
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]\\
\\ \\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.9.tar.gz|^smartsvn-macosx-4_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.9.tar.gz|^smartsvn-generic-4_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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<property name="body"><![CDATA[h3.


----
h3. Download and Install Client&nbsp;

To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
To set up the SmartSVN client, run the application.&nbsp; Next, choose "*Project"* from the&nbsp;Main Menu and then click on "*Check Out..."*

This should bring you to the following page:

\\ !Screen_Save_Checkout_small.jpg|align=left!\\
\\
\\

Click on the&nbsp;*"Manage"* button, create&nbsp;and edit a new profile called&nbsp;*"MBARI_SVN"*&nbsp;as follows:

\\ !Screen_Saver_Edit_Repo_small.jpg|align=left!\\
\\ {color:#ff0000}{*}NOTE\!\!&nbsp;*{color} Make sure you use your own personal *Login Name* when creating this profile and check that the *"Verify connection when pressing 'OK'"* box is clicked in order to verify that your computer is able to connect with the SVN server kahuna.
\\
\\
\\
Once you have&nbsp;properly set up your Profile Name, when you click&nbsp;*"Project"* and *"Check&nbsp;Out..."* from the&nbsp;Main Menu, you should see a&nbsp;a page to login to your account on the repository.&nbsp; Use your standard MBARI network account to log in.&nbsp; Once you have logged in successfully, you will see a list of all projects&nbsp;on&nbsp;the&nbsp;MBARI SVN&nbsp;Repository.\\

\\
&nbsp;]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [http://dev.mysql.com/downloads/connector/j|MySQL JConnector Site]]]></property>
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<property name="body"><![CDATA[h2.


----
h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

\\
&nbsp;

[SVN Client Software Downloads|CLT:SVN Client Software Downloads] {color:#ff0000}\- Windows, Macs, Linux Systems{color}

[Setting up SVN Client&nbsp;to MBARI SVN Repository|CLT:Setting up SmartSVN]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository] {color:#ff0000}\- Non&nbsp;SVN client&nbsp;method{color}

[View the SVN Repository|http://kahuna.shore.mbari.org/viewvc/?root=svn]

\\
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<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]\\
\\ \\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.9.tar.gz|^smartsvn-macosx-4_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.9.tar.gz|^smartsvn-generic-4_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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<property name="body"><![CDATA[h3.


----
h3. Download and Install Client&nbsp;

To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
To set up the SmartSVN client, run the application.&nbsp; Next, choose "*Project"* from the&nbsp;Main Menu and then click on "*Check Out..."*

This should bring you to the following page:

\\ !Screen_Save_Checkout_small.jpg|align=left!\\
\\
\\

Click on the&nbsp;*"Manage"* button, create&nbsp;and edit a new profile called&nbsp;*"MBARI_SVN"*&nbsp;as follows:

\\ !Screen_Saver_Edit_Repo_small.jpg|align=left!\\
\\ {color:#ff0000}{*}NOTE\!\!&nbsp;*{color} Make sure you use your own personal *Login Name* when creating this profile and check that the *"Verify connection when pressing 'OK'"* box is clicked in order to verify that your computer is able to connect with the SVN server kahuna.
\\
\\
\\
Once you have&nbsp;properly set up your Profile Name, when you click&nbsp;*"Project"* and *"Check&nbsp;Out..."* from the&nbsp;Main Menu, you should see a&nbsp;a page to login to your account on the repository.&nbsp; Use your standard MBARI network account to log in.&nbsp; Once you have logged in successfully, you will see a list of all projects&nbsp;on&nbsp;the&nbsp;MBARI SVN&nbsp;Repository.\\

\\
&nbsp;]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to tweak the web client ui a bit as well.  I cd'd to /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages.  I then edited the webclient.properties file.
## Changed company_home from 'Company Home' to 'MBARI'
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 'User Homes' to the end to try to get them to create the user spaces there instead of in the Company Home.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
 {noformat}]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}\\
\\
h3.

----
h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
\\
\\]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to tweak the web client ui a bit as well.  I cd'd to /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages.  I then edited the webclient.properties file.
## Changed company_home from 'Company Home' to 'MBARI'
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
 {noformat}]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to tweak the web client ui a bit as well.  I cd'd to /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages.  I then edited the webclient.properties file.
## Changed company_home from 'Company Home' to 'MBARI'
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
 {noformat}]]></property>
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<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}\\
\\
h3.

----


h3.
Macintosh



({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
\\
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I also wanted to tweak the web client ui a bit as well.  I cd'd to /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/messages.  I then edited the webclient.properties file.
## Changed company_home from 'Company Home' to 'MBARI'
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added '/${spaces.user_homes.childname}' to the end to try to get them to create the user spaces there instead of in the Company Home.
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
 {noformat}]]></property>
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* \\
\\

\---\-

----\\
h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
\\
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## Copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## Created a new custom-authority-services-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
### Edited the file-servers-custom.xml file and added a new config section
{noformat}
   <!-- Allow guest access to file systems -->
   <config evaluator="string-compare" condition="Filesystem Security">

      <authenticator type="passthru">
         <Server>blizzard.shore.mbari.org</Server>
      </authenticator>

   </config>
{noformat}]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## Copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [^|here]
## Created a new custom-authority-services-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
### Edited the file-servers-custom.xml file and added a new config section
{noformat}
   <!-- Allow guest access to file systems -->
   <config evaluator="string-compare" condition="Filesystem Security">

      <authenticator type="passthru">
         <Server>blizzard.shore.mbari.org</Server>
      </authenticator>

   </config>
{noformat}]]></property>
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* &nbsp;\\ \\

----\\
h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
\\
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	<Server>blizzard.shore.mbari.org</Server>
 	</authenticator>
 	 
 	</config>
 {noformat}]]></property>
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<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* {color:#000000}[{color:#000000}SmartSVN-3.0.9.zip{color}|^smartsvn-win32-setup-nojre-3_0_9.zip]{color}\\

h3.


----
h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
\\
\\]]></property>
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</property>
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<id name="id">622621</id>
<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]
* [SmartSVN-3.0.9.zip|smartsvn-win32-setup-nojre-3_0_9.zip]\\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
\\
\\]]></property>
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</property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure NTLM and LDAP.
## LDAP
## NTLM
### Edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml
#### Commented out the current authentication filter and uncommented the ntlm one so it looks like this
{noformat}
   <filter>
      <filter-name>Authentication Filter</filter-name>
      <!--
      <filter-class>org.alfresco.web.app.servlet.AuthenticationFilter</filter-class>
      -->
      <!-- For Novell IChain support use the following filter -->
      <!-- (Enterprise version only)                          -->
      <!--
        <filter-class>org.alfresco.web.app.servlet.NovellIChainsHTTPRequestAuthenticationFilter</filter-class>
      -->
      
      <!-- For NTLM authentication support use the following filter -->
      <!-- (Enterprise version only)                                -->
      
        <filter-class>org.alfresco.web.app.servlet.NTLMAuthenticationFilter</filter-class>
      
   </filter>
{noformat}
#### Uncommented the three AuthenticationFilter url patterns to turn them on.  Should now look like
{noformat}
   <!-- For NTLM authentication support enable the following mapping -->
   <!-- (Enterprise version only)                                    -->
   
   <filter-mapping>
      <filter-name>Authentication Filter</filter-name>
      <url-pattern>/navigate/*</url-pattern>
   </filter-mapping>
   
   <filter-mapping>
      <filter-name>Authentication Filter</filter-name>
      <url-pattern>/command/*</url-pattern>
   </filter-mapping>

   <filter-mapping>
      <filter-name>Authentication Filter</filter-name>
      <url-pattern>/template/*</url-pattern>
   </filter-mapping>
{noformat}
#### Under the WebDAV Authentication filter, I commented out the current one and uncommented the ntlm one so it looks like:
{noformat}
   <filter>
      <filter-name>WebDAV Authentication Filter</filter-name>
      <!--
      <filter-class>org.alfresco.repo.webdav.auth.AuthenticationFilter</filter-class>
      -->
      <!-- For NTLM authentication support use the following filter -->
      <!-- (Enterprise version only)                                -->
      
        <filter-class>org.alfresco.repo.webdav.auth.NTLMAuthenticationFilter</filter-class>
      
   </filter>
{noformat}
### Copied the ntlm-authentication-context.xml.sample to ntlm-authentication-context.xml and edited
#### Changed the id of the authenticationComponentImpl to authenicationComponent
#### Changed the use-local-server property to false
#### Added the servers property and put blizzard,breeze and whirlwind as ntlm servers
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>

<beans>

    <bean id="authenticationDao" class="org.alfresco.repo.security.authentication.ntlm.NullMutableAuthenticationDao" />

    <!-- The authentication component.                                      -->

    <!-- Use the passthru authentication component to authenticate using    -->
    <!-- user accounts on one or more Windows servers.                      -->
    
    <!-- Properties that specify the server(s) to use for passthru          -->
    <!-- authentication :-                                                  -->
    <!--   useLocalServer   use the local server for authentication         -->
    <!--   domain           use domain controllers from the specified domain-->
    <!--   servers          comma delimted list of server addresses or      -->
    <!--                    names                                           -->
       
    <bean id="authenticationComponent" class="org.alfresco.repo.security.authentication.ntlm.NTLMAuthenticationComponentImpl">
        <property name="useLocalServer">
            <value>false</value>
        </property>
        <property name="servers">
            <value>blizzard.shore.mbari.org,breeze.shore.mbari.org,whirlwind.shore.mbari.org</value>
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="guestAccess">
            <value>true</value>
        </property>
    </bean>
    
</beans>
{noformat}
### Created a new custom-authority-services-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>{noformat}]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">589849</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">7405613</id>
<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]
* [SmartSVN-3.0.9.zip|smartsvn-win32-setup-nojre-3_0_9.zip]

\\
&nbsp;

----
\\

h3.


h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
\\
\\]]></property>
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</property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure NTLM and LDAP.
## LDAP
## NTLM
### Edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml
#### Commented out the current authentication filter and uncommented the ntlm one so it looks like this
{noformat}
   <filter>
      <filter-name>Authentication Filter</filter-name>
      <!--
      <filter-class>org.alfresco.web.app.servlet.AuthenticationFilter</filter-class>
      -->
      <!-- For Novell IChain support use the following filter -->
      <!-- (Enterprise version only)                          -->
      <!--
        <filter-class>org.alfresco.web.app.servlet.NovellIChainsHTTPRequestAuthenticationFilter</filter-class>
      -->
      
      <!-- For NTLM authentication support use the following filter -->
      <!-- (Enterprise version only)                                -->
      
        <filter-class>org.alfresco.web.app.servlet.NTLMAuthenticationFilter</filter-class>
      
   </filter>
{noformat}
#### Uncommented the three AuthenticationFilter url patterns to turn them on.  Should now look like
{noformat}
   <!-- For NTLM authentication support enable the following mapping -->
   <!-- (Enterprise version only)                                    -->
   
   <filter-mapping>
      <filter-name>Authentication Filter</filter-name>
      <url-pattern>/navigate/*</url-pattern>
   </filter-mapping>
   
   <filter-mapping>
      <filter-name>Authentication Filter</filter-name>
      <url-pattern>/command/*</url-pattern>
   </filter-mapping>

   <filter-mapping>
      <filter-name>Authentication Filter</filter-name>
      <url-pattern>/template/*</url-pattern>
   </filter-mapping>
{noformat}
#### Under the WebDAV Authentication filter, I commented out the current one and uncommented the ntlm one so it looks like:
{noformat}
   <filter>
      <filter-name>WebDAV Authentication Filter</filter-name>
      <!--
      <filter-class>org.alfresco.repo.webdav.auth.AuthenticationFilter</filter-class>
      -->
      <!-- For NTLM authentication support use the following filter -->
      <!-- (Enterprise version only)                                -->
      
        <filter-class>org.alfresco.repo.webdav.auth.NTLMAuthenticationFilter</filter-class>
      
   </filter>
{noformat}
### Copied the ntlm-authentication-context.xml.sample to ntlm-authentication-context.xml and edited
#### Changed the id of the authenticationComponentImpl to authenicationComponent
#### Changed the use-local-server property to false
#### Added the servers property and put blizzard,breeze and whirlwind as ntlm servers
#### Added the domain property and set to SHORE. Final file should look like
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>

<beans>

    <bean id="authenticationDao" class="org.alfresco.repo.security.authentication.ntlm.NullMutableAuthenticationDao" />

    <!-- The authentication component.                                      -->

    <!-- Use the passthru authentication component to authenticate using    -->
    <!-- user accounts on one or more Windows servers.                      -->
    
    <!-- Properties that specify the server(s) to use for passthru          -->
    <!-- authentication :-                                                  -->
    <!--   useLocalServer   use the local server for authentication         -->
    <!--   domain           use domain controllers from the specified domain-->
    <!--   servers          comma delimted list of server addresses or      -->
    <!--                    names                                           -->
       
    <bean id="authenticationComponent" class="org.alfresco.repo.security.authentication.ntlm.NTLMAuthenticationComponentImpl">
        <property name="useLocalServer">
            <value>false</value>
        </property>
        <property name="servers">
            <value>blizzard.shore.mbari.org,breeze.shore.mbari.org,whirlwind.shore.mbari.org</value>
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="guestAccess">
            <value>true</value>
        </property>
        <property name="domain">
        	<value>SHORE</value>
        </property>
    </bean>
    
</beans>
{noformat}
### Created a new custom-authority-services-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>{noformat}]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">589848</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">7405612</id>
<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]
* [SmartSVN-3.0.9.zip|smartsvn-win32-setup-nojre-3_0_9.zip]

\\
&nbsp;

h3. \\
\\
\\
\\


----
\\

h3.


h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
\\
\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">7372844</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">622618</id>
<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## Copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes.
## Created a new custom-authority-services-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
### Edited the file-servers-custom.xml file and added a new config section
{noformat}
   <!-- Allow guest access to file systems -->
   <config evaluator="string-compare" condition="Filesystem Security">

      <authenticator type="passthru">
         <Server>blizzard.shore.mbari.org</Server>
      </authenticator>

   </config>
{noformat}]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">589851</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">7405611</id>
<property name="body"><![CDATA[\\

\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]
* SmartSVN-3.0.9.zip\\

\\
&nbsp;

h3. \\ \\ \\ \\

----
\\


h3.


h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.3.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.3.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
\\
\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">7372843</id>
</property>
</object>
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<id name="id">622617</id>
<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure NTLM and LDAP.
## LDAP
## NTLM
### Edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml
#### Commented out the current authentication filter and uncommented the ntlm one so it looks like this
{noformat}
   <filter>
      <filter-name>Authentication Filter</filter-name>
      <!--
      <filter-class>org.alfresco.web.app.servlet.AuthenticationFilter</filter-class>
      -->
      <!-- For Novell IChain support use the following filter -->
      <!-- (Enterprise version only)                          -->
      <!--
        <filter-class>org.alfresco.web.app.servlet.NovellIChainsHTTPRequestAuthenticationFilter</filter-class>
      -->
      
      <!-- For NTLM authentication support use the following filter -->
      <!-- (Enterprise version only)                                -->
      
        <filter-class>org.alfresco.web.app.servlet.NTLMAuthenticationFilter</filter-class>
      
   </filter>
{noformat}
#### Uncommented the three AuthenticationFilter url patterns to turn them on.  Should now look like
{noformat}
   <!-- For NTLM authentication support enable the following mapping -->
   <!-- (Enterprise version only)                                    -->
   
   <filter-mapping>
      <filter-name>Authentication Filter</filter-name>
      <url-pattern>/navigate/*</url-pattern>
   </filter-mapping>
   
   <filter-mapping>
      <filter-name>Authentication Filter</filter-name>
      <url-pattern>/command/*</url-pattern>
   </filter-mapping>

   <filter-mapping>
      <filter-name>Authentication Filter</filter-name>
      <url-pattern>/template/*</url-pattern>
   </filter-mapping>
{noformat}
#### Under the WebDAV Authentication filter, I commented out the current one and uncommented the ntlm one so it looks like:
{noformat}
   <filter>
      <filter-name>WebDAV Authentication Filter</filter-name>
      <!--
      <filter-class>org.alfresco.repo.webdav.auth.AuthenticationFilter</filter-class>
      -->
      <!-- For NTLM authentication support use the following filter -->
      <!-- (Enterprise version only)                                -->
      
        <filter-class>org.alfresco.repo.webdav.auth.NTLMAuthenticationFilter</filter-class>
      
   </filter>
{noformat}
### Copied the ntlm-authentication-context.xml.sample to ntlm-authentication-context.xml and edited
#### Changed the id of the authenticationComponentImpl to authenicationComponent
#### Changed the use-local-server property to false
#### Added the servers property and put blizzard,breeze and whirlwind as ntlm servers
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>

<beans>

    <bean id="authenticationDao" class="org.alfresco.repo.security.authentication.ntlm.NullMutableAuthenticationDao" />

    <!-- The authentication component.                                      -->

    <!-- Use the passthru authentication component to authenticate using    -->
    <!-- user accounts on one or more Windows servers.                      -->
    
    <!-- Properties that specify the server(s) to use for passthru          -->
    <!-- authentication :-                                                  -->
    <!--   useLocalServer   use the local server for authentication         -->
    <!--   domain           use domain controllers from the specified domain-->
    <!--   servers          comma delimted list of server addresses or      -->
    <!--                    names                                           -->
       
    <bean id="authenticationComponent" class="org.alfresco.repo.security.authentication.ntlm.NTLMAuthenticationComponentImpl">
        <property name="useLocalServer">
            <value>false</value>
        </property>
        <property name="servers">
            <value>blizzard.shore.mbari.org,breeze.shore.mbari.org,whirlwind.shore.mbari.org</value>
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="guestAccess">
            <value>true</value>
        </property>
    </bean>
    
</beans>
{noformat}
### Created a new custom-authority-services-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
### Edited the file-servers-custom.xml file and added a new config section
{noformat}
   <!-- Allow guest access to file systems -->
   <config evaluator="string-compare" condition="Filesystem Security">

      <authenticator type="passthru">
         <Server>blizzard.shore.mbari.org</Server>
      </authenticator>

   </config>
{noformat}]]></property>
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]\\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.9.tar.gz|smartsvn-macosx-4_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.9.tar.gz|^smartsvn-generic-4_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
\\
\\
\\
\\
\\
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]
* [SmartSVN-3.0.9.zip|smartsvn-win32-setup-nojre-3_0_9.zip]\\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.9.tar.gz|smartsvn-macosx-4_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.9.tar.gz|^smartsvn-generic-4_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
\\
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\\
SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]
* [SmartSVN-3.0.9.zip|smartsvn-win32-setup-nojre-3_0_9.zip]\\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.9.tar.gz|^smartsvn-macosx-4_0_3.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.9.tar.gz|^smartsvn-generic-4_0_3.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure NTLM and LDAP.
## LDAP
## NTLM
### Edited the /opt/alfresco.2.0/tomcat/webapps/alfresco/WEB-INF/web.xml
#### Commented out the current authentication filter and uncommented the ntlm one so it looks like this
{noformat}
   <filter>
      <filter-name>Authentication Filter</filter-name>
      <!--
      <filter-class>org.alfresco.web.app.servlet.AuthenticationFilter</filter-class>
      -->
      <!-- For Novell IChain support use the following filter -->
      <!-- (Enterprise version only)                          -->
      <!--
        <filter-class>org.alfresco.web.app.servlet.NovellIChainsHTTPRequestAuthenticationFilter</filter-class>
      -->
      
      <!-- For NTLM authentication support use the following filter -->
      <!-- (Enterprise version only)                                -->
      
        <filter-class>org.alfresco.web.app.servlet.NTLMAuthenticationFilter</filter-class>
      
   </filter>
{noformat}
#### Uncommented the three AuthenticationFilter url patterns to turn them on.  Should now look like
{noformat}
   <!-- For NTLM authentication support enable the following mapping -->
   <!-- (Enterprise version only)                                    -->
   
   <filter-mapping>
      <filter-name>Authentication Filter</filter-name>
      <url-pattern>/navigate/*</url-pattern>
   </filter-mapping>
   
   <filter-mapping>
      <filter-name>Authentication Filter</filter-name>
      <url-pattern>/command/*</url-pattern>
   </filter-mapping>

   <filter-mapping>
      <filter-name>Authentication Filter</filter-name>
      <url-pattern>/template/*</url-pattern>
   </filter-mapping>
{noformat}
#### Under the WebDAV Authentication filter, I commented out the current one and uncommented the ntlm one so it looks like:
{noformat}
   <filter>
      <filter-name>WebDAV Authentication Filter</filter-name>
      <!--
      <filter-class>org.alfresco.repo.webdav.auth.AuthenticationFilter</filter-class>
      -->
      <!-- For NTLM authentication support use the following filter -->
      <!-- (Enterprise version only)                                -->
      
        <filter-class>org.alfresco.repo.webdav.auth.NTLMAuthenticationFilter</filter-class>
      
   </filter>
{noformat}
### Copied the ntlm-authentication-context.xml.sample to ntlm-authentication-context.xml and edited
#### Changed the use-local-server property to false
#### Added the servers property and put blizzard,breeze and whirlwind as ntlm servers
#### Added the domain property and set to SHORE. Final file should look like
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>

<beans>

    <bean id="authenticationDao" class="org.alfresco.repo.security.authentication.ntlm.NullMutableAuthenticationDao" />

    <!-- The authentication component.                                      -->

    <!-- Use the passthru authentication component to authenticate using    -->
    <!-- user accounts on one or more Windows servers.                      -->
    
    <!-- Properties that specify the server(s) to use for passthru          -->
    <!-- authentication :-                                                  -->
    <!--   useLocalServer   use the local server for authentication         -->
    <!--   domain           use domain controllers from the specified domain-->
    <!--   servers          comma delimted list of server addresses or      -->
    <!--                    names                                           -->
       
    <bean id="authenticationComponentImpl" class="org.alfresco.repo.security.authentication.ntlm.NTLMAuthenticationComponentImpl">
        <property name="useLocalServer">
            <value>false</value>
        </property>
        <property name="servers">
            <value>blizzard.shore.mbari.org,breeze.shore.mbari.org,whirlwind.shore.mbari.org</value>
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="guestAccess">
            <value>true</value>
        </property>
        <property name="domain">
        	<value>SHORE</value>
        </property>
    </bean>
    
</beans>
{noformat}
### Created a new custom-authority-services-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>{noformat}]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4.

# I downloaded and installed BEA's JRocket JVM to use for this installation.
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 4.3.9 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco.2.0
# I then moved the tar into the alfresco.2.0 directory
# I cd'd into that directory and untarred it.
# I downloaded the mysql JDBC driver from [MySQL JConnector Site|http://dev.mysql.com/downloads/connector/j] and put it in my home directory (I don't want all the stuff from the download, just the JAR)
# I then cd'd into the mysql driver directory and copied the mysql-connector-java-5.0.5-bin.jar file to the /opt/alfresco.2.0/tomcat/common/lib directory
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco.2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.1 for linux.
# I kept the download in my home directory and gunzip and untarred it there (there is an install script).
{note}
I hit a snag here as the OpenOffice RPMs needed krb5 and some X11 stuff and I did not have easy access to the install media or prey, so I just skipped this for now.
{note}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco to house the data
## I cd'd to /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco.2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco.2.0
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
]]></property>
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
\\

----
h3. *SmartSVN GUI Installation Files*


----
h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]\\
\\ \\

----
\\

h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.9.tar.gz|^smartsvn-macosx-4_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
\\
\\

----
h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.9.tar.gz|^smartsvn-generic-4_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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There are&nbsp;two recommended CVS Clients to access the MBARI CVS Respository including:&nbsp;{color:#ff0000}{*}WinCVS{*}{color} and {color:#ff0000}{*}SmartCVS{*}{color}.&nbsp;&nbsp; Both clients work for all major operating systems including Windows, Macintosh, and Linux systems.&nbsp;The key bits of information to use when setting up either client are the following:
* User&nbsp; (Your MBARI user/e-mail&nbsp;account, e.g., _salamy_)
* Repository Server (MBARI CVS Repository is hosted on *{_}moonjelly{_}*)
* CVSROOT (*_/home/cvs{_}*)

Thus, the full CVSROOT path for user _salamy_ would be:&nbsp;&nbsp;&nbsp; salamy@moonjelly:/home/cvs&nbsp;

----
\\

h3. *CVS Client&nbsp;Installation Files*


h4. {color:#ff0000}WinCVS{color}

* [WinCVS-1.2.0.zip|^WinCvs120.zip] *\-* {color:#0066cc}{*}Windows{*}{color}
* [MacCVS-3.3b1.dmg|CLT:CVS Client Software Downloads^MacCvsX-3.3b1.dmg] *\-* {color:#0066cc}{*}Macintosh{*}{color}
* [gCVS-1.0-1.i386.rpm|CLT:CVS Client Software Downloads^gcvs-1.0-1.i386.rpm] *\-* {color:#0066cc}{*}Linux (Red Hat)*{color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS-Win32-6.0.8.zip|^smartcvs-win32-setup-nojre-6_0_8.zip] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}(Requires JRE 1.4.1 or higher){color}
* [SmartCVS-MacOS-6.0.8.tar.gz|^smartcvs-macosx-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Macintosh{*}{color} {color:#0066cc}(Requires&nbsp;OS X v. 10.4&nbsp;or higher){color}
* [SmartCVS-Linux-6.0.8.tar.gz|^smartcvs-generic-6_0_8.tar.gz] *\-* {color:#0066cc}{*}Linux{*}{color}

h4.


----
h3. CVS Client Set-Up Instructions


h4. {color:#ff0000}{*}WinCVS{*}{color}

* [Setting up WinCVS-1.2.0.doc|^Setting_up_WinCVS_1.2_new.doc] *\-* {color:#0066cc}{*}Windows{*}{color} {color:#0066cc}({color}{color:#0066cc}{*}NOTE:*{color}{color:#0066cc}&nbsp;Setup same for MacCVS and gCVS as well){color}\\

h4. &nbsp;


h4. {color:#ff0000}SmartCVS{color}

* [SmartCVS Getting-Started Tutorial|^smartcvs-tutorial.pdf] \-&nbsp;{color:#0066cc}{*}PDF Document{*}{color}

----
h3. CVS Administrative Information

* [CVS Admin Notes.doc|^CVS_Source_Code_Repository.doc] \- {color:#ff0000}NOTE: Password Access Required{color}

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<property name="body"><![CDATA[h3.


----
h3. Download and Install Client&nbsp;

To install the SmartSVN client, first download the file from the [SVN Client Software Downloads|CLT:SVN Client Software Downloads] Page and install on your computer.&nbsp;

\\
&nbsp;

h3. Setting up SmartSVN to see the SVN repository on Kahuna

\\
To set up the SmartSVN client, run the application.&nbsp; Next, choose "*Project"* from the&nbsp;Main Menu and then click on "*Check Out..."*

This should bring you to the following page:

\\ !Screen_Save_Checkout_small.jpg|align=left!\\
\\
\\

Click on the&nbsp;*"Manage"* button, create&nbsp;and edit a new profile called&nbsp;*"MBARI_SVN"*&nbsp;as follows:

\\ !Screen_Saver_Edit_Repo_small.jpg|align=left!\\
\\ {color:#ff0000}{*}NOTE\!\!&nbsp;*{color} Make sure you use your own personal *Login Name* when creating this profile and check that the *"Verify connection when pressing 'OK'"* box is clicked in order to verify that your computer is able to connect with the SVN server kahuna.
\\
\\
\\
Once you have&nbsp;properly set up your Profile Name, when you click&nbsp;*"Project"* and *"Check&nbsp;Out..."* from the&nbsp;Main Menu, you should see a&nbsp;a page to login to your account on the repository.&nbsp; Use your standard MBARI network account to log in.&nbsp; Once you have logged in successfully, you will see a list of all projects&nbsp;on&nbsp;the&nbsp;MBARI SVN&nbsp;Repository.\\

\\
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# ADCP: Acoustic Doppler Current Profiler - a sonar that attempts to produce a record of water current velocities for a range of depths [http://en.wikipedia.org/wiki/Acoustic_Doppler_Current_Profiler]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AMQP: Advanced Message Queuing Protocol - [http://www.amqp.org]
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ARI-WG: Access to Remote Instrumentation in a distributed environment - Working Group. OpenGrid Forum [http://www.ogf.org/gf/group_info/view.php?group=ari-wg]
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIAUV:&nbsp; Benthic Imaging Autonomous underwater vehicle
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Bye: in sports and other competitive activities, most commonly refers to the practice of allowing a player or team to advance to the next round of a playoff tournament without playing
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CENIC: The Corporation for Education Network Initiatives in California&nbsp; [http://www.cenic.org/]
# CFD: Computational Fluid Dynamics
# CGSN: Coastal & Global Scale Nodes - [http://www.whoi.edu/ooi_cgsn/home]
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Coolpix: Not an acronym. A registered trademark of Nikon. Digital cameras sold by Nikon, Inc. Coolpix images are digital images captured by a Coolpix camera. We often use the term Coolpix when we mean digital image captured by a digital still camera.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# CREON: {color:black}Coral Reef Environmental Observatory Network&nbsp;{color} {color:black}[http://www.coralreefeon.org/]{color}
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CUAHSI: Consortium of Universities for the Advancement of Hydrologic Science, Inc. - [http://www.cuahsi.org/]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# D-ESP:&nbsp; Deep ESP; the sphere and all it's accouterments
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DSL:&nbsp; Digital Subscriber Line;&nbsp; used to describe a type of modem
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# DWSM:&nbsp; Deep Water Sampling Module
# EarthCube: EarthCube is a NSF activity to create a data and knowledge management system for the 21st Century. The scientific objective is to develop a framework over the next decade to understand and predict the Earth system from the sun to the center of the Earth [http://earthcube.ning.com/]
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPA: Environmental Protection Agency - [http://www.epa.gov/]
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The third 'second generation' ESP instrument
## Bruce Another 'second generation' ESP instrument
## MOE A second gen. instrument with the MFB connected
## Betty&nbsp; \-another one
## Gordon&nbsp; \-another one (Betty & Gordon named after the founders of the Moore Foundation, who funded the builds)
# ESSIN: Earth Sciences Semantic Interoperability Network. A multi-institutional proposal to NSF under the Community-based Data Interoperability Networks (INTEROP) Crosscutting program.
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# FVGR: Free Vehicle Grab Respirometer
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument. It tells you what and where things were printed on the filter paper.
# GNB: Gaussian Naïve Bayes. GNB is a probabilistic classifier relying on Bayes rule to estimate posterior probabilities of labels given the data. Naive assumption in it is an independence of the features. See [http://en.wikipedia.org/wiki/Naive_bayes] for more information.
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. [http://en.wikipedia.org/wiki/Grid_computing]
# GUI: Graphical User Interface
# GWT: Google Web Toolkit - [http://code.google.com/webtoolkit/]
# HDF: Hierarchical Data Format
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# HPP:&nbsp; High-Pressure pump
# ICAN: The International Coastal Atlas Network - [http://ican.science.oregonstate.edu/home]
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# ICPR: International Conference on Pattern Recognition. This is the annual conference of the International Association for Pattern Recognition
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# IMDIS: International Conference on Marine Data and Information Systems sponsored by [http://www.seadatanet.org/]
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# ISUS:&nbsp; In Situ Ultraviolet Spectrophotometer
# IWCE: International Wireless Communication Expo ([http://www.iwceexpo.com])
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JEE: Java Enterprise Edition (formerly known as J2EE)
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# JVM: Java Virtual Machine - [http://en.wikipedia.org/wiki/Jvm]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MB/CA Current: a MBARI project in 2011
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MMI ORR: MMI Ontology Registry and Repository [http://mmisw.org/orr/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MODIS: Moderate Resolution Imaging Spectroradiometer is a key instrument aboard the Terra (EOS AM) and Aqua (EOS PM) satellites.
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MRG: Red Hat Enterprise MRG is a next-generation IT infrastructure incorporating Messaging, Realtime, and Grid functionality. It offers increased performance, reliability, interoperability, and faster computing for enterprise customers. [http://www.redhat.com/mrg/&nbsp];
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# MVC: Model-View-Controller software pattern - [http://en.wikipedia.org/wiki/Model%E2%80%93view%E2%80%93controller]
# NAB: National Association of Broadcasters
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCAR: The National Center for Atmospheric Research [http://www.ncar.ucar.edu/]
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# nctoolbox: nctoolbox is a Matlab toolbox that provides read-only access to common data model datasets. (See [http://code.google.com/p/nctoolbox/])
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NGDC: National Geophysical Data Center [http://www.ngdc.noaa.gov/]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NOAA: National Oceanic and Atmospheric Administration. [http://www.noaa.gov]
# NODC: National Oceanographic Data Center - [http://www.nodc.noaa.gov/]
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTP: Network Time Protocol - a protocol to synchronize the clocks of computers over a network. [http://www.ntp.org/]
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. [http://www.oceansites.org/]
# ODI:&nbsp; Ocean Design Inc.; makers of incredibly expensive underwater connectors
# ODV: Ocean Data View [http://www.oceansites.org/]
# ODSS: Oceanographic Decision Support System
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort - [http://www.oostethys.org/ogc-oceans-interoperability-experiment]
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOI CI: Ocean Observatories Initiative CyberInfrastructure: [http://ci.oceanobservatories.org/] (Developers site: [http://ooici.net/])
# OOR: Open Ontology Repository initiative - [http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# OPeNDAP: The Open-source Project for a Network Data Access Protocol, the protocol used to deliver data directly from the web into user's application workspaces [http://opendap.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SCI: Semantic Collaboration Infrastructure. A multi-institutional proposal to NSF under SI2-SSI (Software Infrastructure for Sustained Innovation, Scientific Software).
# SCPI: Self Contained Plankton Imager, an MBARI project in 2011
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SENSORIS: Sensor Data Integration System. A multi-institutional NSF project under Software Development for Cyberinfrastructure (SDCI) Data Improvement (Office of Cyberinfrastructure)
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIMPA: Seafloor Imaging of Marine Protected Areas. A software tool produced under MBARI projects 900821and 901016.
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SOSC: Smart Ocean Sensors Consortium [http://www.rbr-global.com/about-rbr/rbr-news/124-rbr-joins-sosc?lang=]
# SPARQL - Simple Protocol and RDF Query Language
# SPE:&nbsp; Solid-phase extraction; method from removing DNA or RNA from a 'soup'
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SRVI: Schmidt Research Vessel Institute
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# STOQS: Spatial Temporal Oceanographic Query System - product of the [2010 Upper Water Column Data Visualization project |https://oceana.mbari.org/confluence/display/UpperWaterColumnDataVis]
# SURA: The Southeastern Universities Research Association
# SURF Center:&nbsp; Sensors for Underwater Research of the Future
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TDS: THREDDS Data Server, an application server used to aggregated and enhance the metadata of other OPeNDAP data sources [http://www.unidata.ucar.edu/projects/THREDDS/]
# TERCOM: Terrain Contour Matching
# THREDDS: Thematic Realtime Environmental Distributed Data Services [http://www.unidata.ucar.edu/projects/THREDDS/]
# TREX: Autonomy group mission planning/scheduling software
# TRN: Terrain-Relative Navigation. Using sensors that can "read" nearby terrain and comparing that with a known map of the area to determine where you are.
# TVS:&nbsp; Transient voltage suppressor--special type of diode that protects against over-voltage conditions
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# URI: Uniform Resource Identifier - [http://www.ietf.org/rfc/rfc2396.txt]
# URN: Uniform Resource Name - [http://www.ietf.org/rfc/rfc2141.txt]
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VAAP: Video Annotation Analysis and Presentation [http://www.mbari.org/rd/projects/2010/information.htm]
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# W3C: The World Wide Web Consortium. [http://www.w3.org/]
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WCS: Web Coverage Service
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
# XSD - XML Schema Definition [http://en.wikipedia.org/wiki/XML_Schema]]]></property>
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SmartSVN is the recommended SVN GUI client software to access the MBARI SVN Repository on kahuna.
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h3. *SmartSVN GUI Installation Files*


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h3. *Windows*

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-4.0.9.zip|^smartsvn-win32-setup-nojre-4_0_9.zip]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-3.0.9.zip|^smartsvn-win32-setup-nojre-3_0_9.zip]\\
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h3. Macintosh

({color:#ff0000}Note: all require Mac&nbsp;OS X, version 10.4 or higher{color})
* [SmartSVN-macosx-4.0.9.tar.gz|^smartsvn-macosx-4_0_9.tar.gz]&nbsp;&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-macosx-3.0.9.tar.gz|^smartsvn-macosx-3_0_9.tar.gz]\\
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h3. Linux

({color:#ff0000}Note: all require JRE 1.4.1 or higher{color})
* [SmartSVN-generic-4.0.9.tar.gz|^smartsvn-generic-4_0_9.tar.gz]&nbsp;{color:#ff0000}*\- NEW\!*{color}
* [SmartSVN-generic-3.0.9.tar.gz|^smartsvn-generic-3_0_9.tar.gz]&nbsp;
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h3. Subversion

SVN (Subversion) is a tool used by many software developers to manage changes within their source code tree. SVN provides the means to store not only the current version of a piece of source code, but a record of all changes (and who made those changes) that have occurred to that source code. Use of SVN is particularly common on projects with multiple developers, since SVN ensures changes made by one developer are not accidentally removed when another developer posts their changes to the source tree.

In order to access a Subversion repository, you must install a special piece of software called a Subversion client. Subversion clients are available for most any operating system. Information about the official subversion client can be found at [http://subversion.tigris.org/]. Excellent documentation on using Subversion can be found at [http://svnbook.red-bean.com/]

The&nbsp;MBARI SVN&nbsp;repository may also simply&nbsp;be "viewed" from a web browser for any users who wish to look at its existing source code tree structure at&nbsp;[http://kahuna.shore.mbari.org/viewvc/?root=svn].

\\
&nbsp;

[SVN Client Software Downloads|CLT:SVN Client Software Downloads] {color:#ff0000}\- Windows, Macs, Linux Systems{color}

[Setting up SVN Client&nbsp;to MBARI SVN Repository|CLT:Setting up SmartSVN]

[Adding your code to MBARI's SVN Source Code Repository|CLT:Adding your code to MBARI's SVN repository] {color:#ff0000}\- Non&nbsp;SVN client&nbsp;method{color}

[View the SVN Repository|http://kahuna.shore.mbari.org/viewvc/?root=svn]

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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.254.0
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.255.255
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Make sure startup/shutdown script in /etc/init.d is working correctly
# I.S. then setup backup regime to do incremental backups nightly and full backups weekly]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.254.0
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# TODO: Integrate with OpenOffice
# Setup backup
## On the server, mysql 5 was already installed as a service (whoo-hoo!).
## The first thing to do is to turn on binary logging.  This is done when the mysql service is started.  On oceana, the startup script is /etc/init.d/mysql.  I vi'd the script and added the binary log option to the actual startup command.  So I changed:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" >/dev/null 2>&1 &
{noformat}
to:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" --log-bin=/data/mysql_logs/oceana-bin --log-bin-index=/data/mysql_logs/oceana-bin-idx >/dev/null 2>&1 &
{noformat}
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.254.0
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as 'admin/admin'.
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# TODO: Integrate with OpenOffice
# Setup backup
## On the server, mysql 5 was already installed as a service (whoo-hoo!).
## The first thing to do is to turn on binary logging.  This is done when the mysql service is started.  On oceana, the startup script is /etc/init.d/mysql.  I vi'd the script and added the binary log option to the actual startup command.  So I changed:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" >/dev/null 2>&1 &
{noformat}
to:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" --log-bin=/data/mysql_logs/oceana-bin --log-bin-index=/data/mysql_logs/oceana-bin-idx >/dev/null 2>&1 &
{noformat}
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.254.0
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Setup startup/shutdown script in /etc/init.d and link to one of the rcX.d levels
# Setup backup
## On the server, mysql 5 was already installed as a service (whoo-hoo!).
## The first thing to do is to turn on binary logging.  This is done when the mysql service is started.  On oceana, the startup script is /etc/init.d/mysql.  I vi'd the script and added the binary log option to the actual startup command.  So I changed:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" >/dev/null 2>&1 &
{noformat}
to:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" --log-bin=/data/mysql_logs/oceana-bin --log-bin-index=/data/mysql_logs/oceana-bin-idx >/dev/null 2>&1 &
{noformat}
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.254.0
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Setup startup/shutdown script in /etc/init.d and link to one of the rcX.d levels
# Setup backup
## On the server, mysql 5 was already installed as a service (whoo-hoo!).
## The first thing to do is to turn on binary logging.  This is done when the mysql service is started.  On oceana, the startup script is /etc/init.d/mysql.  I vi'd the script and added the binary log option to the actual startup command.  So I changed:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" >/dev/null 2>&1 &
{noformat}
to:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" --log-bin=/data/mysql_logs/oceana-bin --log-bin-index=/data/mysql_logs/oceana-bin-idx >/dev/null 2>&1 &
{noformat}
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.254.0
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
## OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
### Startup IE.
### Go to Tools->Internet Options ...
### Click on Security tab
### Click on "Trusted Sites" zone
### Click on Sites button
### Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
### Click on close
### Make sure "Trusted Sites" is still selected.
### Click on "Custom Level..." under Security level for this zone.
### Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
### Click on OK
### Click on the "Local Intranet" zone.
### Click on "Custom Level..." under Security level for this zone.
### Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
### Click on OK
### Click on OK to close Internet Options dialog.
## Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
### Take this [here|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed. Find the alfresco-web-client.jar file and copy it to ./WEB-INF/lib.  Delete the existing web-client.jar file in the ./WEB-INF/lib directory and rename the alfresco-web-client.jar to web-client.jar.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Setup startup/shutdown script in /etc/init.d and link to one of the rcX.d levels
# Setup backup
## On the server, mysql 5 was already installed as a service (whoo-hoo!).
## The first thing to do is to turn on binary logging.  This is done when the mysql service is started.  On oceana, the startup script is /etc/init.d/mysql.  I vi'd the script and added the binary log option to the actual startup command.  So I changed:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" >/dev/null 2>&1 &
{noformat}
to:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" --log-bin=/data/mysql_logs/oceana-bin --log-bin-index=/data/mysql_logs/oceana-bin-idx >/dev/null 2>&1 &
{noformat}
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.254.0
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take this [here|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
## Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/images/logo/alfresco_community_horiz20.gif";
{noformat}
## Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
## Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
## Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
## Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Setup startup/shutdown script in /etc/init.d and link to one of the rcX.d levels
# Setup backup
## On the server, mysql 5 was already installed as a service (whoo-hoo!).
## The first thing to do is to turn on binary logging.  This is done when the mysql service is started.  On oceana, the startup script is /etc/init.d/mysql.  I vi'd the script and added the binary log option to the actual startup command.  So I changed:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" >/dev/null 2>&1 &
{noformat}
to:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" --log-bin=/data/mysql_logs/oceana-bin --log-bin-index=/data/mysql_logs/oceana-bin-idx >/dev/null 2>&1 &
{noformat}
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.254.0
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take this [here|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
## Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
## Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
## Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
## Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
## Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Setup startup/shutdown script in /etc/init.d and link to one of the rcX.d levels
# Setup backup
## On the server, mysql 5 was already installed as a service (whoo-hoo!).
## The first thing to do is to turn on binary logging.  This is done when the mysql service is started.  On oceana, the startup script is /etc/init.d/mysql.  I vi'd the script and added the binary log option to the actual startup command.  So I changed:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" >/dev/null 2>&1 &
{noformat}
to:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" --log-bin=/data/mysql_logs/oceana-bin --log-bin-index=/data/mysql_logs/oceana-bin-idx >/dev/null 2>&1 &
{noformat}
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[I had already setup Alfresco 1.3 before writing up these installation instructions.  1.3 had some issues and so I upgraded to 2.0 and included those installation instructions here.  I first setup a test installation on the machine prey to make sure it could do all we wanted it to.  I originally wrote these instructions for the install on prey and then updated them as I installed on oceana (production server).

In order to install Alfresco, I needed Java and a database installed.  On the original installation, I used a database on Solstice (MSSQL) as this was our institutional database server.  One of Alfresco's big draw back was its performance and I suspect it might have had something to do with a remote database.  For that reason, I installed Alfresco so it was a completely local installation using MySQL as the database server.  Prey is a Itanium II server running RedHat Enterprise 4. Oceana is an AMD Opteron box running RHE4.

# I downloaded and installed BEA's JRockit JVM to use for this installation. (J2SE 5)
# I downloaded Alfresco 2.0 from alfresco.org (the tar.gz file and moved it to /opt)
# MySQL was already installed in RHE4 so I was good there (MySQL version 5.0.27).  I simply turned on the mysql service.
# At first there is no root password on mysql, so I changed it using the 'mysql' utility like so (Note the password was removed here.):
{noformat}
[root@prey ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5 to server version: 5.0.27-standard

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> use mysql;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> UPDATE user SET password=PASSWORD('*******') WHERE User='root' and Host='localhost';
Query OK, 1 row affected (0.02 sec)
Rows matched: 1  Changed: 1  Warnings: 0

mysql> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

mysql>
{noformat}
# Now I enabled root access from my desktop so I could use the MySQL Admin GUI like so:
{noformat}
mysql> GRANT USAGE ON *.* TO 'root'@'skagit.shore.mbari.org' IDENTIFIED BY '********';
Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# BTW, PHP 5.1.4 was already installed (this is optional for Alfresco)
# I cd'd to the /opt directory and gunzipped the alfreco tar.gz file
# I created a directory for alfresco as the tar.gz file does not have a base directory.  I created a directory called alfresco-2.0
# I then moved the tar into the alfresco-2.0 directory
# I cd'd into that directory and untarred it.
# In order to setup the DB on the mysql server, I cd'd to the /opt/alfresco-2.0/extras/databases/mysql directory and started up 'mysql -u root -p' and ran
{noformat}
mysql> source db_setup.sql
Query OK, 1 row affected (0.01 sec)

Query OK, 0 rows affected (0.00 sec)

Query OK, 0 rows affected (0.00 sec)

mysql> 
{noformat}
# The database is now created and the appropriate permissions are given to a user name 'alfresco' with password 'alfresco'.  That should be fine for now.
# I did the optional OpenOffice install by visting openoffice.org and downloading verion 2.2 for linux.
## This may not always be the case, but I had a previous install of OpenOffice which I wanted to remove first
### I first ran 'rpm -qa | grep openoffice > rmlist' which gave me a list of all rpms with openoffice in them.
### I looked over the list to make sure I really wanted to remove everything in that list (I did) and then ran 'rpm -e `cat rmlist`'
## I kept the download in my home directory as this will be an RPM based install
## I unzipped the download
## I untarred the download (this created an OOF680_m14_native_packed-1_en-US.9134 directory)
## I cd'd into the new directory and then into the RPMS directory
## I already had java installed, so I moved the jre-6-linux-i596.rpm out of this directory
## I then installed the OpenOffice core by running 'rpm -Uvh --prefix /opt/openoffice-2.2/ *.rpm'
## It said I was missing two dependencies (libgnomevfs and libgconf), but they look like they are located in /usr/lib64. Since I think I have them, I ran the previous command with --nodeps appended to skip dependency checking
## I then cd'd into the desktop-integration directory and executed
### rpm -Uvh openoffice.org-redhat-menus-2.2-9119.noarch.rpm
## Now run /opt/openoffice-2.2/program/soffice to get the GUI interface which will allow you to register soffice (run this as the user that will be running alfresco/soffice)
## Exit OpenOffice
## Run OpenOffice in headless mode to make sure it runs. Before you run OpenOffice in headless mode you may have to actually install Xvfb so you can run from the command line (I leave that to you to figure out).
### /usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16 &
### /opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -
display :1
## Cntl-C out of soffice (assuming it ran)
## Now cd to /opt/alfresco-2.0 and rename the zstart_oo.sh to start_oo.sh and edit so that it looks like the following:
{noformat}
#!/bin/sh
# ---------------------------------------------------------------------------
# Start script for the OpenOffice transform service
# ---------------------------------------------------------------------------
export DISPLAY=:1
echo "Starting Xvfb..."
`/usr/bin/Xvfb -fp /usr/share/X11/fonts/misc :1 -screen 0 800x600x16` &

echo "Starting OpenOffice service..."

# Comment or uncomment the appropriate location using #
# Assumes OpenOffice is installed in /opt
/opt/openoffice-2.2/program/soffice "-accept=socket,host=localhost,port=8100;urp;StarOffice.ServiceManager" -nologo -headless -nofirststartwizard -display :1 &
{noformat}
# In order to make sure Alfresco was using the MySQL installation, I removed the following files from the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extenstion directory:
{noformat}
custom-db-and-data-context.xml
custom-db-connection.properties
custom-hibernate-dialect.properties
{noformat}
# Now before running, I want to make sure the configuration points to the right location where the data will be stored and the database connections.
## I created a directory /data/alfresco-2.0 to house the data
## I cd'd to /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions
## I copied the custom-repository-context.xml.sample to custom-repository-context.xml
## I copied the custom-repository.properties.sample to custom-repository.properties
## I edited the custom-repository.properties file:
### Set the dir.root=/data/alfresco-2.0/data
### Uncommented the db.* properties and left as is (that is the way I set them up)
### Uncommented db.schema.update=true
### Uncommented the two MySQL connection lines and changed the driver to 'com.mysql.jdbc.Driver'
### I also added the following lines at the end of the file to connect up to the external mail server
{noformat}
# 
# The external email server properties
#
mail.host=mail.shore.mbari.org
mail.port=25
mail.username=
mail.password=
{noformat}
### Saved the file
## I copied custom-hibernate-dialect.properties.sample to custom-hibernate-dialect.properties
## I edited the custom-hibernate-dialect.properties file and uncommented the MySQL Dialect line
# I then cd'd back to the /opt/alfresco-2.0 directory and edited the alfresco.sh script and change the APPSERVER to point to the correct directory of /opt/alfresco-2.0
{note}
In the tomcat version of alfresco, the actual alfresco deployment is in a .war file in the tomcat/webapps directory.  If the server has been started, the .war gets expanded into a directory and you could make changes to the files there, but if the war file was ever "touched" again, it would redeploy those file and overwrite your changes.  That is why it is best to make the changes in the .war file so they are permanent
{note}
# Copy the /opt/alfresco-2.0/tomcat/webapps/alfresco.war file to your home directory
# cd to your home directory and make another copy so you will have the original (something like alfresco.war.orig)
# Now I created a new directory called 'scratch' and moved the war there so that it was a clean directory for expansion.  I moved the alfresco.war file to that directory, cd'd to it and then ran 'jar -xvf alfresco.war'.  This expands the contents of the war file (like tar).
# I also wanted to change the "Company Home" that seems to be everywhere.
## Edited ./WEB-INF/classes/alfresco/messages/webclient.properties and changed company_home from 'Company Home' to 'MBARI'
## Edited ./WEB-INF/classes/alfresco/messages/webclient_en_US.properties and changed company_home from 'Company Home' to 'MBARI'
## I edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces.properties and changed the first two lines to read
{noformat}
spaces.company_home.name=MBARI
spaces.company_home.description=The root space for MBARI
{noformat}
## Edited ./WEB-INF/classes/alfresco/messages/bootstrap-spaces_en_US.properties and made the same changes as the previous step
{note}
This took a bit to find all these, and to be honest, I am not sure which one actually made the change on the GUI, but I suspect it was the _en_US ones.
{note}
# When users are imported via LDAP, user spaces get created automatically.  In order to put them where I wanted them to go (instead of right in the Company Home), I edited the ./WEB-INF/classes/alfresco/authentication-services-context.xml file.  In the file there is a bean with an name of personalHomeFolderProvider.  There is a property name 'path' and I added 
{noformat}
/${spaces.user_homes.childname}
{noformat}
to the end to try to get them to create the user spaces there instead of in the Company Home.
# I wanted to change the logo that is used.  I attached the replacement logo [here|^AlfrescoLogo32.png]. Copy this to ./images/logo and overwrite the one that is there.
# In order to setup SSL for the application (will do that later), edit ./WEB-INF/web.xml and add the following
{noformat}
   <!-- Added this security constraint to allow for SSL protection -->
   <security-constraint>
      <web-resource-collection>
         <web-resource-name>Login Pages</web-resource-name>
         <url-pattern>/*</url-pattern>
      </web-resource-collection>
      <user-data-constraint>
         <transport-guarantee>CONFIDENTIAL</transport-guarantee>
      </user-data-constraint>
   </security-constraint>
{noformat}
# In order to configure CIFS server, I edited the file ./WEB-INF/classes/alfresco/file-servers.xml
## I added 'domain="SHORE' to the <host ...> tag.
## I made sure the domain broadcast submask was 255.255.254.0
## I uncommented the WINS section and changed it to
{noformat}
      <WINS>
         <primary>134.89.10.32</primary>
         <secondary>134.89.12.87</secondary>
      </WINS>
{noformat}
## I deleted the enterprise authenticator and replaced it with this:
{noformat}
 	<config evaluator="string-compare" condition="Filesystem Security">
 	    <authenticator type="passthru">
 	        <Server>blizzard.shore.mbari.org</Server>
                <Domain>shore</Domain>
 	    </authenticator>
 	</config>
{noformat}
# OK, this is a total HACK and needed to be done due to the wonderful world of open source.  In Internet Explorer with SSL turned on, you would get a dialog pop-up that stated the secure server was trying to serve non-secure content. This was due to the Alfresco Community logo being served from http://www.alfresco.com. Only IE did this and you can work around it on the client end by doing the following:
## Startup IE.
## Go to Tools->Internet Options ...
## Click on Security tab
## Click on "Trusted Sites" zone
## Click on Sites button
## Make sure check box for "Require Server verification (https:) for all sites in this zone" is unchecked 7. Type in "http://www.alfresco.com" into the "Add this website to the zone:" text field and click Add.
## Click on close
## Make sure "Trusted Sites" is still selected.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on the "Local Intranet" zone.
## Click on "Custom Level..." under Security level for this zone.
## Scroll down till you find the option that says "Display Mixed Content" and select "Enable"
## Click on OK
## Click on OK to close Internet Options dialog.
# Now there are a couple of reasons why this is bad, but the main one is that if you are trying to reach this from outside the firewall, you will have to change those settings for the Internet Zone (I think) which is bad.  Plus every user will have to do this.  To get around this, I had to:
## Take [this|^alfresco_community_horiz20.gif] logo image and save it to ./images/logo directory.
## This next step can either be very easy or very complicated.  You can try downloading [this|^a0.jar] jar file and copying it to ./WEB-INF/lib.  If when you start up Alfresco you get some exceptions that look like they are related to a class called PageTag, you will have to do it the hard way:
### Now you have to actually check out the subversion source code from Alfresco.  I am assuming you know how to do that.  By the way, you will need ant and java installed to do this.  The SVN URL for the repository is svn://www.alfresco.org/alfresco.
### Once it is checked out find the PageTag.java file (should be in HEAD/root/projects/web-client/source/java/org/alfresco/web/ui/repo/tag directory) and edit:
#### Change the line
{noformat}
   private final static String ALF_LOGO  = "http://www.alfresco.com/images/alfresco_community_horiz20.gif";
{noformat}
to:
{noformat}
   private final static String ALF_LOGO  = "/alfresco/images/logo/alfresco_community_horiz20.gif";
{noformat}
### Save the file.
{warning}
If you run this next step on the machine where the application is installed and have a TOMCAT_HOME environment variable defined, it will try to deploy everything to your Tomcat installation.  The best thing to do is build this on a separate machine.
{warning}
### Open a command prompt in the HEAD/root directory and type "ant build-tomcat".  After a long wait, the build will actually fail if you don't have a TOMCAT_HOME defined in your environment.
### Once the build has failed you will need to create a new jar file called a0.jar with only the PageTag.class file in it.
### Copy the a0.jar file to the ./WEB-INF/lib directory.
# That takes care of all the changes to the WAR file.  We can now put it back into .war form.
# You should still have a alfresco.war file in the directory where you ran the jar -xvf command.  Delete or move that file out as you will be recreating it.
# While you are in the directory you expanded the war file in, run
## jar cvfm alfresco.war META-INF/MANIFEST.MF .
# You should now have an alfresco.war file in the directory.  Move that back to the alfreco install and overwrite the existing one.
## mv alfresco.war /opt/alfresco-2.0/tomcat/webapps
# Most users like the details view, so I set the default to that by editing /opt/alfresco.2.0/tomcat/shared/classes/alfresco/extensions/web-client-config-custom.xml and added:
{noformat}
<!-- MBARI Custom: Added this to change the default view to details -->
<config evaluator="string-compare" condition="Views">
      <!-- the views available in the client -->
      <views>
         <!-- default values for the views available in the client -->
         <view-defaults>
            <browse>
               <!-- allowable values: list|details|icons -->
               <view>details</view>
               <page-size>
                  <list>20</list>
                  <details>20</details>
                  <icons>20</icons>
               </page-size>
            </browse>
         </view-defaults>
      </views>
</config>
{noformat}
# Now in order to use MBARI accounts, I needed to configure LDAP.
{note}
In the older version of Alfresco, I actually used NTLM to manage logins, but currently 2.0's NTLM for ActiveDirectory is broken.  The supposedly have fixed it in the Enterprise version, but it has not made it to the Community edition yet.  That is OK, as I will just use LDAP to authenticate.
{note}
## I cd'd to the /opt/alfresco-2.0/tomcat/shared/classes/alfresco/extensions directory
## I then copied the ldap-authentication-context.xml.sample to ldap-authentication-context.xml and edited to match our ActiveDirectory setup.  I have attached the file to this WIKI pages instead of detailing out all the changes. The file is [here|^ldap-authentication-context.xml]
## In order to grant certain accounts admin privs, I created a new custom-authority-services-context.xml in the same directory as the ldap-authentication-context.xml file and added
{noformat}
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE beans PUBLIC '-//SPRING//DTD BEAN//EN' 'http://www.springframework.org/dtd/spring-beans.dtd'>
<beans>
    <bean id="authorityService" class="org.alfresco.repo.security.authority.AuthorityServiceImpl">
        <property name="authenticationComponent">
            <ref bean="authenticationComponentImpl" />
        </property>
        <property name="personService">
            <ref bean="personService" />
        </property>
        <property name="nodeService">
            <ref bean="nodeService" />
        </property>
        <property name="authorityDAO">
            <ref bean="authorityDAO" />
        </property>
        <property name="permissionServiceSPI">
            <ref bean="permissionServiceImpl" />
        </property>
        <property name="adminUsers">
            <set>
    			<value>kgomes</value>
    			<value>admin</value>
    			<value>administrator</value>
    		</set>
        </property>
    </bean>
</beans>
{noformat}
## In the same directory, I edited the file-servers-custom.xml file and added a new config section
{noformat}
 	<!-- Allow guest access to file systems -->
 	<config evaluator="string-compare" condition="Filesystem Security">
 	 
 	<authenticator type="passthru">
 	    <Server>blizzard.shore.mbari.org</Server>
            <Domain>shore</Domain>
 	</authenticator>
 	 
 	</config>
{noformat}
# Now, it is time to setup the server so we can login over SSL.
## In a shell run the keytool and answer the questions as shown (note the first and last name must be the fully qualified host name where alfresco will be run)
{noformat}
kgomes$ sudo keytool -genkey -alias tomcat -keyalg RSA
Enter keystore password:  alfresco
What is your first and last name?
  [Unknown]:  skana.shore.mbari.org
What is the name of your organizational unit?
  [Unknown]:  MBARI
What is the name of your organization?
  [Unknown]:  Monterey Bay Aquarium Research Institute
What is the name of your City or Locality?
  [Unknown]:  Moss Landing
What is the name of your State or Province?
  [Unknown]:  CA
What is the two-letter country code for this unit?
  [Unknown]:  US
Is CN=mbari.org, OU=MBARI, O=Monterey Bay Aquarium Research Institute, L=Moss Landing, ST=CA, C=US correct?
  [no]:  yes

Enter key password for <tomcat>
        (RETURN if same as keystore password):  
{noformat}
This will generate a .keystore file in your home directory.
## Now edit the /opt/alfresco.2.0/tomcat/conf/server.xml. Locate the <Connector> element with port of 8443 and uncomment that section.  Also add the keystorePass="alfresco" phrase.  It should look like
{noformat}
    <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
    <Connector port="8443" maxHttpHeaderSize="8192"
               maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
               enableLookups="false" disableUploadTimeout="true"
               acceptCount="100" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS" keystorePass="alfresco"/>
{noformat}
# I then started alfreso with './alfresco.sh start'
{note}
This takes a couple minutes as it has to first build the DB and all the indexes and such.
{note}
{warning:title=Wait 5 minutes}
After you start up Alfresco with LDAP turned on, it takes 5 minutes before it will import users and groups from Active Directory, so go get a cup of coffee.
{warning}
# Then I can go to the web interface at http://prey.mbari.org:8080/alfresco and login as your MBARI username.
# TODO: Setup startup/shutdown script in /etc/init.d and link to one of the rcX.d levels
# Setup backup
## On the server, mysql 5 was already installed as a service (whoo-hoo!).
## The first thing to do is to turn on binary logging.  This is done when the mysql service is started.  On oceana, the startup script is /etc/init.d/mysql.  I vi'd the script and added the binary log option to the actual startup command.  So I changed:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" >/dev/null 2>&1 &
{noformat}
to:
{noformat}
 /usr/bin/mysqld_safe  --defaults-file=/etc/my.cnf --pid-file="$mypidfile" --log-error="$errlogfile" --log-bin=/data/mysql_logs/oceana-bin --log-bin-index=/data/mysql_logs/oceana-bin-idx >/dev/null 2>&1 &
{noformat}
# TODO: Setup backup for data directory and for alfresco install directory.]]></property>
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<property name="body"><![CDATA[# AAAI: Association for the advancement of artificial intelligence
# ACT: Alliance for Coastal Technology. A NOAA-funded partnership of research institutions, resource managers, and private sector companies dedicated to fostering the development and adoption of effective and reliable sensors and platforms. [http://www.act-us.info/]
# AEITS: Autonomous Eye-in-the Sea - stand-alone deepwater video observatory for unobtrusive monitoring (not connected to a cable - gathers data autonomously)
# AGU: American Geophysical Union
# AIV: Analytical Instrument Valve (a valve on the MFB)
# Alfresco: not an acronym. Open source content management system. [http://www.alfresco.com] [http://alfresco.mbari.org]
# ALOHA-MARS: [http://alohamooring.apl.washington.edu/] ALOHA (A Long-term Oligotrophic Habitat Assessment) is a place off the coast of Hawaii where HOT (Hawaiian Ocean Timeseries) Station 2 data is taken, at 22 45'N, 158W, located about 100 km north of Oahu, Hawaii. Station ALOHA has been the location of \~monthly shipboard observations of water column physics, biogeochemistry, and ecosystems for over 18 years. Nearby moorings have also been deployed (e.g. HALE-ALOHA). The NSF-funded cabled observatory deployed at that site is called the ALOHA observatory.  MARS is the Monterey Advanced Research System (see below). The idea is to deploy a mooring in Monterey Bay connected to the MARS observatory, and in the future another one at the ALOHA site connected to the ALOHA observatory. The team hopes to deploy subsequent similar nodes at other observatory sites (H20, Neptune, DEOS sites, etc.). [http://seahurst.apl.washington.edu/mars.php]
# AMC: Autonomous Mission Controller
# AOA: Angle of Attack
# APL: Applied Physics Laboratory, University of Washington
# ASLO: American Society of Limnology and Oceanography
# ASTEP: Astrobiology Science and Technology for Exploring Planets
# ATS: Autonomous Tissue Sampler
# AVED: Automated Visual Event Detection [http://www.mbari.org/aved/]
# AWW: All was well. [http://www.jkrowling.com/en/]
# Beowulf cluster: scalable performance collection of independent computers based on commodity hardware, on a private system network, with open source software (Linux) infrastructure.
# BIOSA: Biophysical Oceanographic Sensor Array
# Bogey: not an acronym. A score of one over par on any individual hole.
# BOM: Bill of Materials
# BRS/MRS: Benthic Respirometer System / Midwater Respriometer System [http://www.mbari.org/expeditions/Pulse53/gear.htm]
# Calit2: California Institute for Telecommunications and Information Technology (at UCSD)
# Caltech: California Institute of Technology [http://en.wikipedia.org/wiki/Caltech]
# CDR: Critical Design Review ("Hey I'm starting to build something, should I stop?")
# CI: Cyberinfrastructure [http://en.wikipedia.org/wiki/Cyberinfrastructure]
# CeNCOOS: Central and Northern California Ocean Observing System [http://www.cencoos.org/]
# CFD: Computational Fluid Dynamics
# CMORE: Center for Microbial Oceanography: Research and Education (a funding source)
# CNAME'd: canonical name, also referred to as a CNAME record, a record in a DNS database that indicates the true, or canonical, host name of a computer that its aliases are associated with. an alias so that DNS can resolve some alias to a specific machine [http://www.webopedia.com/TERM/C/CNAME.htm]
# COI: Common operating infrastructure (one of seven projects that together implement the Network for Ocean Research, Interaction and Application (NORIA) OOI CI.
# Condor: not an acronym. A specialized workload management system for compute-intensive jobs developed by the University of Wisconsin-Madison [http://www.cs.wisc.edu/condor/]
# Cron: not an acronym.  Cron is the name of program that enables UNIX users to execute commands or scripts (groups of commands) automatically at a specified time/date. [http://www.unixgeeks.org/security/newbie/unix/cron-1.html]
# CTD: Conductivity, Temperature, and Depth [http://www.whoi.edu/instruments/viewInstrument.do?id=1003]
# CVS: Concurrent Versions System; maintains control of history of code/documents
# DataNet solicitation: NSF 07-601, Sustainable Digital Data Preservation and Access Network Partners (DataNet).
# DC: Dublin Core vocabulary
# DEM: Digital Elevation Model
# DI: De-ionized, often used with water
# DMO: Division of Marine Operations
# DMZ: Demilitarized zone. Computers placed into their own subnetwork (sometimes protected by a back-end firewall) in direct connection with the internet, protected by a front-end firewall. [http://en.wikipedia.org/wiki/Demilitarized_zone_(computing])
# Doc Ricketts: ROV, replacing Tiburon, carried by R/V Western Flyer.
# DOEST: Day of Engineering, Science and Technology
# Dribbling: not an acronym. The act of bouncing the ball continuously
# DStoNetCDF: SSDS post-processing service
# DVL: Doppler Velocity Log
# EE: Electrical Engineering
# eGY: the Electronic Geophysical Year [http://www.egy.org/]
# EITS: Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring. [http://www.mbari.org/mars/general/eits.html]
# EOM: Electro-Optical-Mechanical
# EPIC: Embedded Platform for Industrial Computing
# ERA: Earned Run Average
# ESB: Enterprise Service Bus
# ESIP Federation: Federation of Earth Science Information Partners
# ESONET: European Seafloor Observatory Network [http://www.oceanlab.abdn.ac.uk/research/esonet.php]
# ESP: Environmental Sample Processor - Chris Scholin et al. [http://www.mbari.org/muse/platforms/ESP.htm]
## Darlene was the 1st generation ESP
## GiGi The first 'second generation' ESP instrument
## NEO 'Nasa-Earth-Observatory'; The second 'second generation' ESP instrument
## Mack The 'third generation' ESP instrument
## Bruce Another 'third generation' ESP instrument
## MOE A third gen. instrument with the MFB connected
# Et al.: and others
# FC5: Fedora Core 5
# FDR: Final Design Review
# Ferret: plotting/analysis software package
# FOCE: Free Ocean CO2 Enrichment
# FPGA: Field Programmable Gate Array
# FSM: Finite State Machine
# GAL: Gene Array Layout which is the file generated when printing a microarray for the ESP instrument.  It tells you what and where things were printed on the filter paper.
# FVGR: Free Vehicle Grab Respirometer
# GEOSS: Global Earth Observation System of Systems [http://www.epa.gov/geoss/]
# GRID Computing: Grid computing (or the use of a computational grid) is the application of several computers to a single problem at the same time - usually to a scientific or technical problem that requires a great number of computer processing cycles or access to large amounts of data. http://en.wikipedia.org/wiki/Grid_computing
# GUI: Graphical User Interface
# Hexakosioihexekontahexaphobia: not an acronym. Fear of the number six-hundred sixty-six.
# HOBI: Harbor Branch Oceanographic Institution
# HOTS: Hawaii Ocean Time-Series program
# ICD: Interface Control Diagram; block diagram of all system components and their interfaces
# IDE: Integrated Development Environment
# iLab: Professor Laurent Itti's biologically inspired computational modeling group at the University of Southern California. They maintain the iLab Neuromorphic Vision C+\+ Toolkit that we use in AVED for visual event detection.
# International metadata summit: This summit is formally titled the IODE/JCOMM Forum on Oceanographic Data Management and Exchange Standards.  It is a weeklong meeting of a small group (17) of leaders in international oceanographic data and metadata systems, yet is intended to initiate international agreements on metadata standards.  See [http://www.iode.org/index.php?option=com_content&task=view&id=74] for details.
# IO: Implementing Organization [http://www.orionprogram.org/PDFs/OOI_CG_RFP_16Mar07.pdf]
# IOC: Intergovernmental Oceanographic Commission, [http://ioc.unesco.org/iocweb/index.php]
# IODE: International Oceanographic Data Exchange, [http://www.iode.org]
# IODP: Integrated Ocean Drilling Program [http://www.iodp.org]
# IOOS: Integrated and Sustained Ocean Observing System [http://www.ocean.us]
# JCOMM: Joint WMO-IOC Technical Commission on Oceanography and Marine Meteorology, [http://ioc.unesco.org/iocweb/index.php]
# JIRA: A bug tracking, issue tracking, and project management application [http://www.atlassian.com/software/jira/]
# JOI: Joint Oceanographic Institutions [http://www.joiscience.org/joi]
# KML: Keyhole Markup Language - A file format used to display geographic data in an Earth browser, such as Google Earth
# LED: Light-emitting diode
# LDEO: Lamont-Doherty Earth Observatory, Columbia University
# LLNL: Lawrence Livermore National Laboratories
# LRAUV: Long Range AUV (Autonomous Underwater Vehicle)
# LST: Langrangian sediment trap
# MATE: Marine Advanced Technology Education Center at Monterey Peninsula College (MPC)
# MARS: Monterey Accelerated Research System - Monterey Cabled Observatory System
# Maven: software project management and comprehension tool. [http://maven.apache.org/]
# MBA: Monterey Bay Aquarium
# MEITS: Moored Eye-in-the Sea - deepwater video observatory for unobtrusive monitoring to be deployed on MARS
# Meta-T:  Water Temperature metadata pilot project, which is being developed under the umbrella of the Joint WMO-IOC Technical Commission for Oceanography and Marine Meteorology (JCOMM). ([http://marinemetadata.org/meta-t] )
# MFB: Micro-Fluidics Block--added instrumentation to the ESP
# MMI: Marine Metadata Initiative [http://marinemetadata.org/]
# MOBB: Monterey Ocean Bottom Broadband project
# Modbus: a serial [communications protocol|http://en.wikipedia.org/wiki/Communications_protocol] [http://en.wikipedia.org/wiki/Modbus]
# MOOS: Monterey Ocean Observing System [http://www.mbari.org/moos]
# MSE: MOOS Science Experiment
# MTS: Marine Technology Society
# MUCE: Monterey Upper Canyon Experiment
# Mule: not an acronym. Open source ESB. [http://mule.codehaus.org/display/MULE/Home]
# MV: Medium Voltage (converter); located in node power supply of MARS
# Nagios: software to monitor all types of computer and network services. [http://www.nagios.org/]
# Navproc: navigation processor
# NCBO: The National Center for Biomedical Ontology
# NCSA: National Center for Supercomputing Applications (at UIUC)
# NDBC: National Data Buoy Center
# netCDF: file format used for MBARI processed data (stands for Network Common Data Form) [http://www.unidata.ucar.edu/software/netcdf/conventions.html]
# NSF: National Science Foundation
# NMI: NSF Middleware initiative
# NORIA: Network for Ocean Research, Interaction and Application. The OOI CI IO.
# NTR: Nothing To Report
# OA: Obstacle Avoidance
# OBIS: Ocean Biogeographic Information System
# OceanSITES: A worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters. http://www.oceansites.org/
# ODV: Ocean Data View http://www.oceansites.org/
# OGC: Open Geospatial Consortium, Inc.® (OGC), a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services. [http://www.opengeospatial.org/]
# OGC Oceans IE = Open Geospatial Consortium Oceans Interoperability Experiment. It is being hosted by the OOSTethys effort
# OGF: Open Grid Forum, an open community committed to driving the rapid evolution and adoption of applied distributed computing. [http://www.ogf.org/]
# OMF: Observatory Middleware Framework. A project funded by NSF. NCSA is the prime. MBARI is a subcontractor (at about ½ of the grant). UCSD (Frank Vernon) is a non-paid participant.
# OMV: Ontology Metadata Vocabulary
# OMV-MMI: MMI extensions to OMV
# ONR: Office of Naval Research
# OOI: Ocean Observatories Initiative (NSF) [http://www.orionprogram.org/OOI/default.html]
# OOSTethtys: not an acronym. A provider-to-user data systems framework, using interoperable standards, enabling discovery and use of data. [http://www.oostethys.org/]
# ORION: Ocean Research Interactive Observatory Networks [http://www.orionprogram.org]
# PC-104: small microprocessor for embedded systems (can run Linux) [http://www.pc104.org]
# PCA: Principal component analysis. [http://en.wikipedia.org/wiki/Principal_components_analysis]
# PCR: Polymerase Chain Reaction, procedure to make millions of copies of DNA from a few
# PDR: preliminary design review ("Hey, I thought of something.  Is it a stupid idea?")
# PDU: Power Distribution Unit (? not sure about this though)
# pH: a measure of the [acidity|http://en.wikipedia.org/wiki/Acid] or [alkalinity|http://en.wikipedia.org/wiki/Base_%28chemistry%29] of a solution. pH is a shorthand for its mathematical approximation: in chemistry a small p is used in place of writing log10 and the H here represents [H+], the concentration of hydrogen ions. [http://en.wikipedia.org/wiki/PH]
# pl-navproc: the name of a computer
{noformat}
Name:    pl-navproc.pl.mbari.org
Address:  134.89.22.11
{noformat}
we think navproc was the shortened name for navigation processor; we guess, "Point Lobos Navigation Processor".
# PRDK: PUCK Reference Design Kit [http://www.mbari.org/pw]
# PUCK: Pluggable Underwater Connector with Knowledge [http://www.mbari.org/pw]
# PUP: Precision Underwater Positioner
# QNX: A Unix-like real-time operating system
# RAID: Redundant Array of Independent Drives [http://en.wikipedia.org/wiki/RAID]
# RBI: Runs Batted In
# RC: Radio controlled (airplane)
# RCO: Regional Cabled Observatory [http://orionprogram.org/PDFs/RevisedOOICND08Mar07.pdf]
# RDF: W3C Resource Description Framework
# ROS: Remote Ocean Systems [http://www.rosys.com/]
# ROV: Remotely Operated Vehicle
# RS-232 (Recommended Standard 232) is a standard for [serial|http://en.wikipedia.org/wiki/Serial_communications] binary data signals connecting between a DTE ([Data terminal equipment|http://en.wikipedia.org/wiki/Data_terminal_equipment]) and a DCE ([Data Circuit-terminating Equipment|http://en.wikipedia.org/wiki/Data_circuit-terminating_equipment]). It is commonly used in [computer serial ports|http://en.wikipedia.org/wiki/Computer]. [http://en.wikipedia.org/wiki/RS-232]
# RSN: Regional Scale Node. See RCO. [http://www.ooi.washington.edu/rsn/secondary.jsp?keywords=WHATSR&title=What%20is%20RSN?]
# SAP: Single Axis PUP
# SDCI: Software Development for Cyberinfrastructure. A program at NSF.
# SeaDataNet: Multi-national, multi-system data management project funded by the European Union, which will provide metadata, data and products as a unique virtual data centre. ([http://www.seadatanet.org/])
# SensorML: not an acronym; markup language to describe sensors and their data. [http://vast.uah.edu/SensorML/]
# SIFT: Scale-invariant feature transform [http://en.wikipedia.org/wiki/Scale-invariant_feature_transform]
# SIIM: Science Instrument Interface Module
# SIMM: Single In-line Memory Module
# SIO: Scripps Institute of Oceanography
# SMD: Soil Machine Dynamics Hydrovision [http://www.smdhydrovision.com]
# SMP: Symmetric Multiprocessing
# SNMP: (Scripps NCSA MBARI Prototype) a proof of concept project staffed at MBARI as part of SENSORS to integrate instrument network capabilities of SIO and MBARI with a policy management framework provided by NCSA and visualization capabilities provided by Calit2-Viz within an ESB-based integration infrastructure.
# SOPAC: Pacific Islands Applied Geoscience Commission [http://www.sopac.org]
# SOS: Sensor Observation Service, one of the SWE (Sensor Web Enablement) standards
# SPARQL - Simple Protocol and RDF Query Language
# SPS: Sensor Planning Service, one of the SWE (Sensor Web Enablement) standards
# SSDS: Shore-Side Data System [http://www.mbari.org/ssds/] [http://new-ssds.mbari.org:8080/ssds/]
# SURA: The Southeastern Universities Research Association
# SVN: Subversion which is a source code repository.
# SWE: Sensor Web Enablement set of standards (approved by OGC)
# SWE Common: next-generation core for Sensor Web Enablement standards
# TAMU: Texas A&M University
# TERCOM: Terrain Contour Matching
# TREX: Autonomy group mission planning/scheduling software
# TWIC: Transportation Worker Identification Credential (TWIC™) [http://www.tsa.gov/what_we_do/layers/twic/index.shtm]
# UART: universal asynchronous receiver/transmitter, a type of "asynchronous receiver/transmitter", a piece of [computer|http://en.wikipedia.org/wiki/Computer] [hardware|http://en.wikipedia.org/wiki/Hardware] that translates data between parallel and serial interfaces. [http://en.wikipedia.org/wiki/UART]
# UCB: University of California-Berkeley
# UCSB: University of California, Santa Barbara
# UCSD: University of California, San Diego
# UI: User Interface
# UIUC: University of Illinois at Urbana-Champaign
# UNOLS: University-National Oceanographic Laboratory System.  An organization of [61 academic institutions|http://www.unols.org/info/direct.html] and National Laboratories involved in oceanographic research and joined for the purpose of coordinating oceanographic ships' schedules and research facilities.
# UPS: Uninterrupted Power Supply
# UUST: Unmanned Untethered Submersible Technology Symposium [http://www.ausi.org/uust/uust.html]
# UW: University of Washington
# VARS: Video Annotation and Reference System. [http://vars.sourceforge.net/]
# VB: Variable Buoyancy
# VB: Visual Basic
# VCS: Vehicle Control System
# VENUS: Victoria Experimental Network Under the Sea. A cabled ocean observatory. [http://www.venus.uvic.ca/]
# VHDL: VHSIC (Very-High-Speed Integrated Circuit) Hardware Description Language
# VINE:  Vocabulary INtegration Environment
# Voc2RDF: Vocabulary to RDF conversion tool
# WATERS Network: WATer and Environmental Research Systems Network (WATERS Network)
# WFS: Web Feature Service
# WHOI: Woods Hole Oceanographic Institute
# WMO: World Meteorology Organization, [http://www.wmo.ch]
# WMS: Web Map Service
# WNS: Wet node simulator (MARS observatory simulation environment)
# XML: Extensible Markup Language [http://en.wikipedia.org/wiki/XML]
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