Difference between revisions of "OBO-Edit: Getting the Source Code"

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==Running OBO-Edit From Eclipse==
 
==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  
 
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  

Revision as of 10:34, 18 October 2007

Introduction

OBO-Edit is stored in a subversion repository within the Gene Ontology sourceforge project.

Dependencies

OBO-Edit is based on two important libraries, the OBO API and the BBOP Java API. Modifications to OBO-Edit may require modifications to these two supporting libraries as well. Therefore, it is strongly suggested that you check out the source code for all three libraries when working with OBO-Edit.

Getting the Source Code with Eclipse

Build Paths

The OBO-Edit Eclipse project is designed to be used with the OBO API and BBOP Java API. The build path in the OBO-Edit project file refers to projects named "OBO" and "BBOP" as dependencies, so it is highly recommended that you follow the optional instructions below to create these projects as well.

However, this is not necessary. If you prefer, you may check out only the OBO-Edit project, remove the project dependencies, and modify the build path to include lib/runlibs/bbop.jar and lib/runlibs/obo.jar instead.

Installing Subversion Support

Current versions of Eclipse do not automatically support subversion. However, the subclipse plugin adds seamless subversion support to Eclipse, using the existing Team mechanisms. See http://subclipse.tigris.org/install.html for installation instructions.

Getting OBO-Edit from Subclipse

  1. Choose File -> New -> Project
  2. Select "Checkout Projects from SVN" in the New Project Wizard, and click "Next"
  3. Choose "Create a New Repository Location" and click "Next"
  4. Enter https://geneontology.svn.sourceforge.net/svnroot/geneontology/java/oboedit/ into the location field and click "Next"
  5. Choose the trunk directory to get the latest version (choose a branch from the "tags" or "branches" directories to get an earlier version) and click "Next"
  6. Enter a name for the Eclipse project ("OBO-Edit" is recommended) and click "Finish"

(Optional) Getting the OBO API from Subclipse

  1. Choose File -> New -> Project
  2. Select "Checkout Projects from SVN" in the New Project Wizard, and click "Next"
  3. Choose "Create a New Repository Location" and click "Next"
  4. Enter https://geneontology.svn.sourceforge.net/svnroot/geneontology/java/obo/ into the location field and click "Next"
  5. Choose the trunk directory to get the latest version (choose a branch from the "tags" or "branches" directories to get an earlier version) and click "Next"
  6. Enter a name for the Eclipse project ("OBO" is recommended) and click "Finish"

(Optional) Getting the BBOP API from Subclipse

  1. Choose File -> New -> Project
  2. Select "Checkout Projects from SVN" in the New Project Wizard, and click "Next"
  3. Choose "Create a New Repository Location" and click "Next"
  4. Enter https://geneontology.svn.sourceforge.net/svnroot/geneontology/java/bbop/ into the location field and click "Next"
  5. Choose the trunk directory to get the latest version (choose a branch from the "tags" or "branches" directories to get an earlier version) and click "Next"
  6. Enter a name for the Eclipse project ("BBOP" is recommended) and click "Finish"

Congratulations! You're done!

Getting the Source Code with Command-Line SVN

Make sure that you have correctly installed Subversion on your computer, change to the desired parent directory and run the following commands:

svn co https://geneontology.svn.sourceforge.net/svnroot/geneontology/java/oboedit/trunk OBO-Edit

To check out the supporting projects, run these additional commands:

svn co https://geneontology.svn.sourceforge.net/svnroot/geneontology/java/bbop/trunk BBOP
svn co https://geneontology.svn.sourceforge.net/svnroot/geneontology/java/obo/trunk OBO

Running OBO-Edit From Eclipse

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

SVN Notify

If you wish to stay informed of every single svn commit, you can use svnnotify via the URL below:

(notes: This page is only accessible to admins of the Gene Ontology sourceforge site. snvnotify will also notify you of changes in other projects. I'm not sure how to do this at a finer level of granularity as yet)