Checkout, Compile, and Test Cytoscape 3 Core on Eclipse

Status

• Document revesion 1.0 release: KeiichiroOno

• Document revesion 1.1 release. Fixed minor issues based on feedback: KeiichiroOno

• Document revesion 1.2 release. OSGi Project Nature section added: KeiichiroOno

• Document revesion 1.2.1 release. VM Argument added for look & feel problem: KeiichiroOno

• Document revesion 1.3.0 release. Tutorial is based on CytoscapeIDE: KeiichiroOno

• Document revesion 1.3.1. Cytoscape IDE plugin is a bit out-of-date, so please install plugins one by one if you have any problems.: KeiichiroOno

• Document revesion 1.4: Updated for Cytoscape IDE 0.1.1. This is not finished yet. Will be ready 5/8/2009: KeiichiroOno (5/7/2009)

Introduction

This tutorial is for Java developers who wants to learn how to checkout code, compile, and test Cytoscape 3 with Eclipse PDE and other Eclipse plugins.

Tutorial

Step 1. Setup Your Environment

To develop Cytoscape 3 on Eclipse, you need to install several software packages.

1. Java Development Kit (JDK)

You need to install JDK version 5 or 6. Should work on both 32 bit and 64 bit versions. I tested this tutorial with the following JDK:

java version "1.6.0_13"
Java(TM) SE Runtime Environment (build 1.6.0_13-b03)
Java HotSpot(TM) Client VM (build 11.3-b02, mixed mode)

I strongly recommend to use Java 6 if it is available for your platform.

2. Eclipse PDE

This tutorial is based on the latest version of Eclipse 3.4, called Ganymede. Several distributions are available on Eclipse web site. In this tutorial, we use Eclipse for RCP/Plug-in Developers version 3.4. This distribution includes PDE (Plugin development environment). I recommend to install latest version of Eclipse PDE to a new directory on your machine. Otherwise, the screenshots may be different due to Eclipse plugins you have already installed on your machine.

You can install Eclipse by just extracting archive file (zip/gzip) to a directoly of your choice. By default, the eclipse directory should look like the following:

To keep your Eclipse up-to-date, you can update plugins by software updater (help-->software updates...)

For Windows Users: Set JDK JVM

Usually, Eclipse for Windows use JRE virtual machine instead of JDK's VM. To use JDK's VM, create a shortcut and edit the shortcut's property:

eclipse.exe -vm "c:¥path to jdk¥bin¥javaw.exe"

3. Cytoscape IDE

You can install all required Elcipse plugins for Cytoscape 3 development at once by installing Cytoscape IDE Plugin for Eclipse.

1. Select Help-->Software Updates...

2. Select Available Software tab

3. Click Add Site button and type http://chianti.ucsd.edu/kono/cyide in the Location text box. Then press OK.

   • 

4. Eclipse automatically scans the location and displays available plugins. You have to choose only one plugin, Cytoscape IDE for Eclipse

   • 

5. Press Install button and follow instructions. This process takes several minutes because it installes lots of plugins at once. When installation is complete, you will be asked to restart Eclipse. Press Yes and restart Eclipse.

6. Select Window-->Open Perspective-->Other. Then you can find Cytoscape IDE as a new perspective. Select it and press OK

   • 

7. If your workspace layout looks like the following, Eclipse is ready to develop Cytoscape 3.

   • 

Note: My Testing Environment

I've tested the following tutorial on these platforms:

• Common
  • Eclipse PDE 3.4.2 Ganymede

• Test Platform 1 (Unix) Confirmed to work

  • RHEL 5 Desktop 64 bit
  • Java SE 6 update 13 64 bit

• Test Platform 2 (Windows) Still have small issues

  • Windows XP SP3 32 Bit

  • JDK SE 6 update 13 Important Note: You should use JDK, not JRE.

• Test Platform 3 (Mac)

Step 2. Checkout and Create Cytoscape 3 Eclipse Project

In this section, you will learn how to create an Eclipse project from the fresh Cytoscape 3 checkout.

Checkout Cytoscape 3 Trunk

1. Start Eclipse. I recommend to use an empty, new workspace only for Cytoscape 3 project since it creates tons of new bundle projects in your workspace. Make sure Cytoscape IDE perspective is selected.

2. Turn off automatic build. (uncheck Project > Build Automatically)

3. Select SVN Repository tab. Cytoscape subversion repository will appear automatically.

4. If you are a core developer, use svn+ssh://grenache.ucsd.edu/common/svn. You need id and pssword. Otherwise, use http://chianti.ucsd.edu/svn. You can checkout the project from this URL, but cannot checkin.

5. The Cytoscape 3 repository is cytoscape3/trunk.

   • 

6. From SVN Repository window, right-click cytoscape3 > trunk and select Check out as Maven project...

7. Select Source Code Management (SCM) system type to svn and make sure the URL is set to http://chianti.ucsd.edu/svn/cytoscape3/trunk (for core developers, svn+ssh://grenache.ucsd.edu/common/svn/cytoscape3/trunk).

8. Make sure Check out All projects checkbox is unchecked. Then click Finish

   • 

   This process takes 5-10 minutes depends on your network connection.

9. You will be asked to select maven projects you want to import. Select top-level pom and application ONLY.

   • 

10. Select Package Explorer tab. Your Eclipse workspace looks like the following:

    • 

Step 3. Build and Run Cytoscape 3 on OSGi Frameworks

• 

  (Cytoscape 3 running on Windows XP + Java 6 update 13 with Nimbus L&F)

First, let's build and run Cytoscape 3 from Eclipse workspace.

1. Select core project on the workspace. Right click and select Run As > Maven install. When you select this command, Eclipse builds and installs Cytoscape 3 bundles to your local maven repository ($HOME/.m2). It takes several minutes to complete (depends on your machine power).

   • 

2. You will see the message in the console if it is successful.

   • 

3. Select Run → Run Configurations

4. Create new Maven Build and name it

5. Set the Base directory to core bundle

6. Set the goal to pax:run

   • 

7. Apply and Run. You can use Felix Shell commands on the console.

   • 

8. Quit Cytoscape

For Windows Users

[FelixStartLevel] DEBUG org.springframework.osgi.extender.internal.activator.ContextLoaderListener - Setting globally defined wait-for-dependencies timeout value=300000 ms, for bundle [org.cytoscape.work-swing-impl (org.cytoscape.work-swing-impl)]
[FelixDispatchQueue] DEBUG cytoscape.application - BundleEvent RESOLVED
[FelixDispatchQueue] DEBUG org.cytoscape.presentation-api - BundleEvent RESOLVED
[FelixDispatchQueue] DEBUG org.cytoscape.splash - BundleEvent RESOLVED
[FelixDispatchQueue] DEBUG org.swinglabs.swing-layout - BundleEvent RESOLVED
[FelixDispatchQueue] DEBUG org.cytoscape.cy-commons-cli - BundleEvent RESOLVED
[FelixDispatchQueue] DEBUG org.cytoscape.viewmodel - BundleEvent RESOLVED
[FelixDispatchQueue] DEBUG org.cytoscape.work-spring-hack - BundleEvent RESOLVED
[FelixDispatchQueue] DEBUG org.cytoscape.io-api - BundleEvent RESOLVED
[FelixDispatchQueue] DEBUG org.cytoscape.work-swing-impl - BundleEvent STARTED
[FelixDispatchQueue] DEBUG org.cytoscape.view.vizmap - BundleEvent RESOLVED
[FelixDispatchQueue] DEBUG org.cytoscape.session-api - BundleEvent RESOLVED

Somehow, you need to press enter several times after the message above if you use Windows. Otherwise, you cannot proceed.

Generate Manifest File for Eclipse PDE

At this point, application project is configured as Maven project. This means you can use m2eclipse plugin's features for the project, such as POM file editor, dependency graph visualization, etc. Since Cytoscape 3 is an OSGi application, actual distribution file (jar file) always include a manifest file MANIFEST.MF, which is a meta data for the OSGi bundle. As you know, all Eclipse plugins are also OSGi bundles, you can use PDE's Manifest editor features for Cytoscape projects. You can configure Cytoscape 3 application project as an PDE project by following the procedure below:

1. Select Run > Run Configurations...

2. Create new Maven Build

3. Name it Generate Manifest for Eclipse

4. Click Browse Workspace and select application project.

5. Set install pax:eclipse for goals

6. Apply and Run.

   • 

7. Once it is done, refresh the workspace (press F5) and/or refresh maven project configuration by selecting Maven ---> Update Maven Configuration. You can see META-INF directory and under the folder, you can find MANIFEST.MF file. This is the metadata

   • 

Editing this metadata file by writing BND statements is beyond the scope of this tutorial and will be discussed later in Plugin Development section. However by using this feature, you can see what packages are available for the selected project (bundle), and what packages will be exported as public API.

Important Note: Maven and PDE

Eclipse PDE has a feature to build OSGi bundle manually. In this case, you need to edit MANIFEST.MF file by hand using PDE's Manifest editor. However, in Cytoscape project, we use to generate MANIFEST-MF automatically. This means, even if you edit MANIFEST.MF file in your Eclipse project, it will not be used when you create bundle! Therefore, you can use PDE's manifest editor as viewer of current manifest file generated by maven plugin, but cannot use it as an editor. You can control the manifest file generation process by editing pom.xml and osgi.bnd. This will be discussed in plugin development documents.

Step 4. Debug Cytoscape 3 on Eclipse with PAX Cursor

In this section, you will learn how to debug Cytoscape 3 on Eclipse.

1. First, let's set a sample break point in CytoscapeInit class, which is the class to startup Cytoscape. It is in application/src/main/java/cytoscape/CytoscapeInit.java. You can set breakpoint anywhere in the public boolean init(CyInitParams params) method.

   • 

     

2. From Eclipse main window, select Run → Debug Configurations

3. Right click on OSGi Framework and select New

4. Name the configuration Cytoscape 3

5. Switch framework to Felix 1.0.4

6. None of the files should be selected in the bundle list

   • 

7. Click Arguments tab

8. Add the following VM Arguments

   -Xbootclasspath/a:bundles/com.jgoodies.looks_2.1.2.jar:bundles/cytoscape-sun.jhall_1.0.0.jar

   • 

9. Click the Pax Cursor tab

10. Click Add Pom. Then select pom file under runner directory. To get the deploy-pom.xml file to show, you have to change the File of type ComboBox to have Any File.

    • 

11. Apply and Debug

    • 

12. Now you can see Cytoscape running on Felix and debugger shows current status of variables

    • 

    Just like other applications, Eclipse debugger stops execution at the break-point you specified in the source code. To start again, you need to press green triangle (Resume button).

    • 

Basically, the debugging process is same as regular Java projects. Once you edit something in the source code, you can rebuild and deploy it to local repository by Maven install command. Then you can repeat the procedure above to check internal states of Cytoscape 3 by Eclipse debugger.

Working with Felix OSGi Console

Cytoscape 3 is an OSGi application and you can check the status of bundles from OSGi console. After you start Cytoscape 3 from Eclipse, you can see a prompt on the Console window (if not, hit enter in the console to show the prompt). The following is some useful command to check internal states of the OSGi system. For more information, please visit [Felix web site].

• help - display help message

  -> help
  bundlelevel <level> <id> ... | <id> - set or get bundle start level.
  cd [<base-URL>]                     - change or display base URL.
  headers [<id> ...]                  - display bundle header properties.
  help                                - display impl commands.
  install <URL> [<URL> ...]           - install bundle(s).
  packages [<id> ...]                 - list exported packages.
  ps [-l | -s | -u]                   - list installed bundles.
  refresh [<id> ...]                  - refresh packages.
  resolve [<id> ...]                  - attempt to resolve the specified bundles.
  services [-u] [-a] [<id> ...]       - list registered or used services.
  shutdown                            - shutdown framework.
  start <id> [<id> <URL> ...]         - start bundle(s).
  startlevel [<level>]                - get or set framework start level.
  stop <id> [<id> ...]                - stop bundle(s).
  uninstall <id> [<id> ...]           - uninstall bundle(s).
  update <id> [<URL>]                 - update bundle.
  version                             - display version of framework.

• ps - List loaded bundles

  -> ps
  START LEVEL 4
     ID   State         Level  Name
  [   0] [Starting   ] [    0] System Bundle (1.0.4)
  [   1] [Active     ] [    4] cytoscape.util.intr [cytoscape] (1.0.0.SNAPSHOT)
  [   2] [Active     ] [    4] cytoscape.graph.fixed [cytoscape] (1.0.0.SNAPSHOT)
  [   3] [Active     ] [    4] cytoscape.graph.dynamic [cytoscape] (1.0.0.SNAPSHOT)
  [   4] [Active     ] [    4] org.cytoscape.network [org.cytoscape] (1.0.0.SNAPSHOT)
  [   5] [Active     ] [    4] cytoscape.render.immed [cytoscape] (1.0.0.SNAPSHOT)
  [   6] [Active     ] [    4] cytoscape.geom.spacial [cytoscape] (1.0.0.SNAPSHOT)
  [   7] [Active     ] [    4] cytoscape.render.stateful [cytoscape] (1.0.0.SNAPSHOT)
  [   8] [Active     ] [    4] cytoscape.geom.rtree [cytoscape] (1.0.0.SNAPSHOT)
  [   9] [Active     ] [    4] cytoscape.render.export [cytoscape] (1.0.0.SNAPSHOT)
  [  10] [Active     ] [    4] org.cytoscape.attributes (1.0.0.SNAPSHOT)
  [  11] [Active     ] [    4] org.cytoscape.tunable (1.0.0.SNAPSHOT)
  [  12] [Active     ] [    4] cytoscape.task [cytoscape] (1.0.0.SNAPSHOT)
  [  13] [Active     ] [    4] phoebe.dnd [phoebe] (1.0.0.SNAPSHOT)
  [  14] [Active     ] [    4] undo (1.0.0.SNAPSHOT)
  [  15] [Active     ] [    4] org.cytoscape.view (1.0.0.SNAPSHOT)
  [  16] [Active     ] [    4] org.apache.commons.cli             [org.apache] (1.0.0.SNAPSHOT)
  [  17] [Active     ] [    4] Apache Commons Lang (2.4.0)
  [  18] [Active     ] [    4] org.cytoscape.layout (1.0.0.SNAPSHOT)
  [  19] [Active     ] [    4] org.cytoscape.vizmap (1.0.0.SNAPSHOT)
  [  20] [Starting   ] [    4] cytoscape.application              [cytoscape] (1.0.0.SNAPSHOT)
  [  21] [Resolved   ] [    4] JDOM DOM Processor (1.0.0)
  [  22] [Resolved   ] [    4] Java Activation API (1.1.0)
  [  23] [Installed  ] [    4] Concurrent (1.3.4)
  [  24] [Resolved   ] [    4] Lowagie iText (2.0.8)
  [  25] [Installed  ] [    4] csplugins.automatic.layout [csplugins] (1.0.0.SNAPSHOT)
   .
   .
   .

• services - show list of available OSGi Services

• services BUNDLE_ID - show detail of services abailable from the bundle

  -> services 25
  
  csplugins.automatic.layout [csplugins] (25) provides:
  -----------------------------------------------------
  name = force-directed
  objectClass = org.cytoscape.layout.CyLayoutAlgorithm
  preferredMenu = Cytoscape Layouts
  service.id = 21
  ----
  name = circular
  objectClass = org.cytoscape.layout.CyLayoutAlgorithm
  preferredMenu = Cytoscape Layouts
  service.id = 22
  ----
  name = hierarchical
  objectClass = org.cytoscape.layout.CyLayoutAlgorithm
  preferredMenu = Cytoscape Layouts
  service.id = 23
  ----
  .
  .
  .

• services -u - show usage of services.

  -> services -u
  
  System Bundle (0) uses:
  -----------------------
  org.osgi.service.startlevel.StartLevel
  
  org.cytoscape.layout (18) uses:
  -------------------------------
  org.cytoscape.layout.CyLayoutAlgorithm
  org.cytoscape.layout.CyLayoutAlgorithm
  org.cytoscape.layout.CyLayoutAlgorithm
  org.cytoscape.layout.CyLayoutAlgorithm
  org.cytoscape.layout.CyLayoutAlgorithm

• services -u BUNDLE_ID - show more detail about service usage of the bundle

  org.cytoscape.layout (18) uses:
  -------------------------------
  name = force-directed
  objectClass = org.cytoscape.layout.CyLayoutAlgorithm
  preferredMenu = Cytoscape Layouts
  service.id = 21
  ----
  name = circular
  objectClass = org.cytoscape.layout.CyLayoutAlgorithm
  preferredMenu = Cytoscape Layouts
  service.id = 22
  ----
  name = hierarchical
  objectClass = org.cytoscape.layout.CyLayoutAlgorithm
  preferredMenu = Cytoscape Layouts
  service.id = 23
  ----
  .
  .
  .

Note: The behaviour of Cytoscpae 3 running on Felix will be different from time to time. This is because budle loading timing is not properly controlled now. This will be solved by organizing bundle/service dependency. I'm working on this issue now and hopefully it will be solved soon.

Notes

Now you are ready to hack Cytoscape 3 on Eclipse. As you can see on your workspace, Cytoscape 3 is a collection of OSGi bundles. Each bundle is built as a Maven project and has a pom.xml file.

Currently, the desktop version of Cytoscape 3 is called application bundle. Under src/main/java you can see the source tree. You can edit these source files just like 2.x series, and create the bundle by running maven commands. To run them, you need to select (right click) the project name and then select maven command from Run As menu:

• maven clean - clean all classes from target directory.
• maven install - build everything under the selected project, create bundles, run tests, and install them to your local Maven repository

To run your modified code, you just need to do maven install and run debugger.

Troubleshooting

1. Somehow Cytoscape 3 Eclipse project is broken and I cannot compile it anymore

   • From terminal, run mvn pax:clean pax:eclipse. This cleans up everything and gives you a fresh workspace.

2. pax:provision fails. What should I do?

   • Cleaning up the working space (maven clean) and rebuilding it (maven install) solves this problem in most cases.

3. Cannot compile application bundle. Eclipse display some warning messages and cannot complete install goal

   • Comment out following lines in pom.xml in core directory:

     • <showWarnings>true</showWarnings>
       <showDeprecation>true</showDeprecation>

     We are working on this problem.

4. Eclipse and Cytoscape are frozen after splashscreen is displayed. What happened?

   • On Windows, somehow Felix shell waits user's key entry after Cytoscape displays splashscreen. To proceed, you need to hit enter key in the console window (see below):

     • 

Appendix

Install Required Eclipse Plugins One by One

Subversion Client (Subclipse)

Cytoscape 3 source code is managed by Subversion. To access the repository, you need to install subversion client for Eclipse. In this tutorial, I'll use Subclipse. You can install the plugin from the eclipse's update manager. Do not forget to install SVNKit. Otherwise, you will get an error message when you try to check out repository ("Unable to load default SVN Client")

You can install the Subclipse plugin from Help > Software Updates... Click Available Software tab and add this URL by pressing Add Site button: http://subclipse.tigris.org/update_1.4.x

PAX Cursor

PAX Cursor is an Eclipse plugin developed by OPS4J developers. Basically, it is an Eclipse integration for PAX-Runner. By this plugin, you can run set of bundles on multiple platforms including Felix, Equinox, and Knopflerfish.

To install this Eclipse plugin, just follow the standard plugin installation procedure discussed above.

• PAX Cursor Eclipse Update Site - http://www.ops4j.org/pax/eclipse/update/

Maven Integration for Eclipse (m2eclipse)

Cytoscape build system has been moved to Maven. To use maven from Eclipse, you need to follow this instruction. Even if you run all maven commands from Eclipse, you still need to install command-line version of Maven since Eclipse embedded version of maven have issues to execute some maven goals.

• m2eclipse plugin update site - http://m2eclipse.sonatype.org/update/

This document is written by KeiichiroOno

If you have any questions, please e-mail me (kono at ucsd dot edu. English or Japanese)