Creating an database of benthic-only annotations

1. Copy solstice:VARS to fog:VARS_Benthic
   • Use the DTS Job on Fog: Copy Solstice:VARS to FOG:VARS_Benthic
   • Brian Schlining: I last ran this on 2008-02-21
2. Check out VARS from Subversion
   • svn co https://vars.svn.sourceforge.net/svnroot/vars/trunk vars
3. Build VARS for the vdm database (located on Fog as VARS_Benthic)
   • mvn clean install -Denvironment=vdm -Dmaven.test.skip=true
   • Fog is updated every night from the VARS database on Solstice. This is a good database to work with since we can make changes and tests without breaking any production systems.
4. Check out the vdm-tools from subversion
   • svn co svn+ssh://kahuna.shore.mbari.org/svn/repos/vdm-tools/trunk vdm-tools
5. Build the project
   • mvn clean package
     • The built applications will be in vdm-tools/target/vdm-tools-<VERSION>.zip
     • Extract the zip file somewhere
6. Add a table to the database you're working with

   • CREATE TABLE [dbo].[VideoFrameMetadata] ( 
         [VideoFrameID_FK]	bigint NOT NULL,
         [Altitude]       	float NOT NULL,
         CONSTRAINT [FK_03] PRIMARY KEY([VideoFrameID_FK])
     )
     GO

7. Find a bathymetry file of the area you want to work with. The tool can read ASCII raster grids or netcdf files. An example netCDF file, monterey_hrbath.nc, is checked into Subversion with the project.
8. cd to the bin directory where you extracted the zip file (from above)
9. Run gsh ../scripts/groovy/createbenthosdb1.groovy
   • For example: gsh ../scripts/groovy/createbenthosdb1.groovy ../../../src/test/resources/monterey_hrbath.nc
   • This populates the table VideoFrameEmbargo with ids of all the VideoFrames within the grid files area and stores the altitudes.
10. Run gsh ../scripts/groovy/createbenthosdb5.groovy
    • This drops all the non-benthic data from the Association, Observation, PhysicalData, CameraData and VideoFrame tables.
    • Brian Schlining: I ran this on 2008-02-21
11. Verify results. Brian Schlining: ongoing