OBO-Edit: Getting Old Source Code from CVS

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Note

As of OBO-Edit 2.000-beta15, the OBO-Edit source code is stored an SVN repository. The instructions on this page are only to be used to retrieve older versions of the OBO-Edit code. See OBO-Edit: Getting the Source Code for instructions on how to fetch the current code.

Getting the Source Code with Eclipse

  1. Choose File -> New -> Project
  2. Select "Project from CVS" in the New Project Wizard, and click "Next"
  3. Choose "Create a New Repository Location" and click "Next"
  4. Enter the information below into the form, and press "Next"
    • Host: geneontology.cvs.sourceforge.net
    • Repository Path: /cvsroot/geneontology
    • User: anonymous (if you have developer access, enter your username)
    • Password: blank (if you have developer access, enter your password)
    • Connection type pserver (if you have developer access, use extssh)
    • Use default port
  5. Select Use specified module name, enter go-dev/java/oboedit in the text field, and click "Next"
  6. Select Check out as a project in the workspace and enter a name for the project (I suggest OBO-Edit)
  7. Make sure Checkout subfolders is selected and press "Next"
  8. Leave Use default workspace location selected and press "Next"
  9. If you want the latest version of OBO-Edit, select HEAD and click "Finish"
  10. If you want the code from an earlier version of OBO-Edit, select Branches and click "Refresh Tags". Expand the "Branches" node and select the desired tag from the list.

Congratulations! You're done!

Note: OBO-Edit makes extensive use of the org.geneontology library. You may want to check out the org.geneontology library sourcecode as well. To do it, follow all the steps above, but enter go-dev/java/org.geneontology in the Use specified module name box. Make sure to create a new project for org.geneontology WITH A DIFFERENT NAME! If you plan to recompile org.geneontology and use the changes in OBO-Edit, you will need to set the "oboedit_library_path" ANT property for your project.

Getting the Source Code with Command-Line CVS

Make sure that you have correctly installed CVS on your computer, and run the following commands:

For anonymous CVS access

cvs -d:pserver:anonymous@geneontology.cvs.sourceforge.net:/cvsroot/geneontology login
cvs -z3 -d:pserver:anonymous@geneontology.cvs.sourceforge.net:/cvsroot/geneontology co -P go-dev/java/oboedit
optional: cvs -z3 -d:pserver:anonymous@geneontology.cvs.sourceforge.net:/cvsroot/geneontology co -P go-dev/java/org.geneontology

For developer CVS access

export CVS_RSH=ssh
cvs -z3 -d:ext:username@geneontology.cvs.sourceforge.net:/cvsroot/geneontology co -P go-dev/java/oboedit

Note that these CVS commands will get you the last version of OBO-Edit that was checked into CVS before the source was moved to SVN--an early version of 2.000-beta. If you want OBO-Edit 1, follow the instructions below.

Running OBO-Edit From Eclipse

In order to run the application you need to link the oboedit and org.geneontology sections. To do this right-click the oboedit package. Choose properties, then build path and then the package tab. You can then browse to your workspace and choose the org.geneontology folder. Click ok.


When you run OBO-Edit you need to assign the amount of memory it will use. To do so choose menu item 'run' and then 'run' from the menu. Then fill in the following parameter in the VM arguments box according to the amount of memory in your computer:

Run options.jpeg


Old Versions

If you want to download old released versions of OBO-Edit for bug fixing then you can do that too. When you check out the main package you get to the window with the hierarchy of versions that says 'branch' at the top. Click 'refresh' and then open the branches bit to see the versions available. Choose the one that you want. You will also need to later import the correct version of org.geneontology. To find out which is the right one try to run OBO-Edit and look at the 'Problems' tab to see what it says. Here it should tell you the dependencies that were not satisfied, including the version of org.geneontology that it wants. Once you find this out you can go back and import the correct version of the org.geneontology package.