Software Infrastructure : Collaboration Tools Home Page

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.

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.

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.

Authentication and Single Sign On With Crowd

Crowd is an authentication tool that is developed by Atlassian 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.

Content Management with 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.

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.

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.

WIKI Collaboration Pages (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.

Issue (bug) tracking (JIRA)

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.

Maven Dependency Repository Maven

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 is a software project management and comprehension tool. Similar to Ant, 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 or Ant (via 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.

Modeling with UML (JBuilder 2008 R2)

Once downloaded and installed, you need to copy the following .slip file to the:

Concurrent Versioning System

CVS (Concurrent Versioning System) is an open source software tool used by software developers to manage code changes within their source code tree. This source code versioning system is the predecessor of Subversion (see below) and applies stricter security access when editing MBARI project files. 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. 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. Without access permission, users may only view and download code - not upload it into the repository to make changes. Access is given to users who are part of that project's group on CVS. To gain a password or access to edit a project requires notification to the server administrator: Karen Salamy (salamy@mbari.org).

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

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

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

Introduction