Diff for "Cytoscape_3/CoreDevelopment/GettingStarted"

Differences between revisions 22 and 24 (spanning 2 versions)

Cytoscape 3 Documentation : Getting Started

Editor(s): SamadLotia

Date: December 5th 2011

Status: First version

Contents

Purpose
Check out, build and run
Modifying a bundle

Purpose

This document covers how to check out the cytoscape 3 source code form cy3 repository, how to build using maven, and how to get Cytoscape 3 running. In addition, it covers how to make your first changes to the core code and then rebuild and run.

Check out, build and run

If you are using Eclipse development environment, please look at this page first.
Check out Cytoscape with Subversion:
1. Public Access (no account required; read-only)
  - svn co http://chianti.ucsd.edu/svn/core3/cy3 cy3
  - This will take a few seconds to start, then will sequentially fetch each subfolder. The entire checkout will take many minutes to complete.
2. Private Access (you must be a Cytoscape developer and have account at grenache.ucsd.edu; read-write access)
  - svn co svn+ssh://grenache.ucsd.edu/cellar/common/svn/core3/cy3 cy3
  - If it's been a while since you last checked anything out, make sure you can ssh into grenache.ucsd.edu before doing a check out to make sure your password has not expired.
  - When using the command line to do a check out:
    - If your local machine's user name differs from your user name on grenache, Subversion may incorrectly switch from using your grenache user name to your local machine's user name, preventing you from completing a check out. To fix this, open ~/.subversion/config and under the [tunnels] section, add this line:
      - ssh = $SVN_SSH ssh -l user-name
    - The above line forces Subversion to call ssh with the -l parameter whenever it does ssh tunneling. Note that you will have to comment out this line if you have to work with another Subversion repository that uses ssh tunneling with a different user name.
    - If you don't want ssh to repeatedly ask for your password, see this: http://oreilly.com/pub/h/66
Do mvn install in cy3/gui-distribution.
Go to cy3/gui-distribution/assembly/target/cytoscape, then run cytoscape.sh if you're on Mac or Linux or cytoscape.bat if you're on Windows.

Modifying a bundle

For isolated changes, at a minimum, you need to...
1. Rebuild the bundles you modify, e.g.,
  - mvn -pl impl/work-impl clean install
2. Then update the bundle via the Cytoscape console:
  - update [bundle id]
  - Note: you can get the bundle id with list|grep [part of bundle name] (more commands)
For more extensive changes and prior to committing changes, you should...
1. Rebuild the bundles you modify and all dependencies, with tests, e.g.,
  - mvn -amd -pl api/work-api impl/work-impl clean install
2. Remove the karaf_data cache and restart Cytoscape:
  - rm -rf ~/CytoscapeConfiguration/3/karaf_data

Cytoscape_3/CoreDevelopment/GettingStarted (last edited 2013-03-21 19:33:45 by 192)

-  ← Revision 22 as of 2012-07-11 23:46:38 →
  Size: 3478
  Editor: server2
  Comment:
+  ← Revision 24 as of 2012-09-05 20:34:10 →
  Size: 3172
  Editor: AlexPico
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 29:
-. Find the bundle you want to modify in either the {{{cy3/api}}} or {{{cy3/impl}}}.
+ * For isolated changes, at a minimum, you need to...

  1. Rebuild the bundles you modify, e.g., 

     {{{mvn -pl impl/work-impl clean install}}}

  1. Then update the bundle via the Cytoscape console:

     {{{update [bundle id]}}} 

     *''Note: you can get the bundle id with'' {{{list|grep [part of bundle name]}}} ''([[http://wiki.cytoscape.org/Cytoscape_3/Interactive_Shell|more commands]])''
-Line 31:
+Line 36:
-. After making a change to the source code, run {{{mvn install}}} within {{{cy3/api}}} or {{{cy3/impl}}}.
-Line 33:
+Line 37:
-. Go back to {{{cy3/gui-distribution}}} and do {{{mvn clean install}}}.

   * If you don't want to recompile all of {{{gui-distribution}}} every time a bundle is modified:

      1. Go to {{{assembly/target/features-repo}}} and copy your newly compiled bundle to the appropriate location. {{{features-repo}}} follows the conventions of a local Maven repository.

      1. Delete {{{cy3/gui-distribution/assembly/target/cytoscape/framework/data/cache}}}

   * Alternatively, you can install your bundle through Karaf console -- Cytosape interactive shell. On the console window, press "Enter" to get command prompt and look at [[http://wiki.cytoscape.org/Cytoscape_3/Interactive_Shell|this page]] for the commands and syntax.

 1. Now running Cytoscape in {{{cy3/gui-distribution/assembly/target/cytoscape}}} should pick up your newly compiled bundle.
+ * For more extensive changes and prior to committing changes, you should...

  1. Rebuild the bundles you modify and all dependencies, with tests, e.g., 

     {{{mvn -amd -pl api/work-api impl/work-impl clean install}}}

  1. Remove the karaf_data cache and restart Cytoscape:

     {{{rm -rf ~/CytoscapeConfiguration/3/karaf_data}}}