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

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==Introduction==
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OBO-Edit is stored in a [http://subversion.tigris.org/project_packages.html subversion] repository within the [http://sourceforge.net/projects/geneontology Gene Ontology sourceforge project].
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==Dependencies==
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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.
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==Getting the Source Code with Eclipse==
 
==Getting the Source Code with Eclipse==
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===Build Paths===
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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.
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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.
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===Installing Subversion Support===
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Current versions of Eclipse do not automatically support subversion. However, the [http://subclipse.tigris.org/ subclipse] plugin adds seamless subversion support to Eclipse, using the existing Team mechanisms. See [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html] for installation instructions.
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===Getting OBO-Edit from Subclipse===
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# Choose File -> New -> Project
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# Select "Checkout Projects from SVN" in the New Project Wizard, and click "Next"
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# Choose "Create a New Repository Location" and click "Next"
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# Enter <code>https://geneontology.svn.sourceforge.net/svnroot/geneontology/java/oboedit/</code> into the location field and click "Next"
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# Choose the <code>trunk</code> directory to get the latest version (choose a branch from the "tags" or "branches" directories to get an earlier version) and click "Next"
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# Enter a name for the Eclipse project ("OBO-Edit" is recommended) and click "Finish"
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===(Optional) Getting the OBO API from Subclipse===
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# Choose File -> New -> Project
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# Select "Checkout Projects from SVN" in the New Project Wizard, and click "Next"
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# Choose "Create a New Repository Location" and click "Next"
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# Enter <code>https://geneontology.svn.sourceforge.net/svnroot/geneontology/java/obo/</code> into the location field and click "Next"
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# Choose the <code>trunk</code> directory to get the latest version (choose a branch from the "tags" or "branches" directories to get an earlier version) and click "Next"
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# Enter a name for the Eclipse project ("OBO" is recommended) and click "Finish"
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===(Optional) Getting the BBOP API from Subclipse===
 
# Choose File -> New -> Project
 
# Choose File -> New -> Project
# Select "Project from CVS" in the New Project Wizard, and click "Next"
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# Select "Checkout Projects from SVN" in the New Project Wizard, and click "Next"
 
# Choose "Create a New Repository Location" and click "Next"
 
# Choose "Create a New Repository Location" and click "Next"
# Enter the information below into the form, and press "Next"
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# Enter <code>https://geneontology.svn.sourceforge.net/svnroot/geneontology/java/bbop/</code> into the location field and click "Next"
#* '''Host:''' <code>geneontology.cvs.sourceforge.net</code>
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# Choose the <code>trunk</code> directory to get the latest version (choose a branch from the "tags" or "branches" directories to get an earlier version) and click "Next"
#* '''Repository Path:''' <code>/cvsroot/geneontology</code>
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# Enter a name for the Eclipse project ("BBOP" is recommended) and click "Finish"
#* '''User:''' <code>anonymous</code> ''(if you have developer access, enter your username)''
 
#* '''Password:''' ''blank'' ''(if you have developer access, enter your password)''
 
#* '''Connection type''' <code>pserver</code> ''(if you have developer access, use <code>extssh</code>)''
 
#* '''Use default port'''
 
# Select '''Use specified module name''', enter <code>go-dev/java/oboedit</code> in the text field, and click "Next"
 
# Select '''Check out as a project in the workspace''' and enter a name for the project (I suggest <code>OBO-Edit</code>)
 
# Make sure '''Checkout subfolders''' is selected and press "Next"
 
# Leave '''Use default workspace location''' selected and press "Next"
 
# If you want the latest version of OBO-Edit, select <code>HEAD</code> and click "Finish"
 
# If you want the code from an earlier version of OBO-Edit, select <code>Branches</code> and click "Refresh Tags". Expand the "Branches" node and select the desired tag from the list.
 
  
 
Congratulations! You're done!
 
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 <code>go-dev/java/org.geneontology</code> 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 SVN==
 
==Getting the Source Code with Command-Line SVN==

Revision as of 14:32, 16 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

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