Running and Developing Cytoscape 3 on Eclipse

Introduction

This is a tutorial document to learn how to run and develop Cytoscape 3 with Eclipse PDE.

Procedure

Setting Up Your Environment

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

Eclipse

This tutorial is based on the latest version of Eclipse 3.4, called Ganymede. Several distributions are available on [http://www.eclipse.org/downloads/packages/ Eclipse web site]. You need to use one of the following:

• Eclipse Classic 3.4
• Eclipse for RCP/Plug-in Developers

Both of these distributions include PDE (Plugin Development Environment).

Subversion

Cytoscape 3 source code is managed by [http://subversion.tigris.org/ Subversion]. To access the repository, you need to install subversion client for Eclipse. In this tutorial, I'll use [http://subclipse.tigris.org/ 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")

Repository locations are the following:

• Core Developers: svn+ssh://grenache.ucsd.edu/common/svn/cytoscape3

• Others: http://chianti.ucsd.edu/svn/cytoscape3/

You need to checkout the trunk directory.

Maven and Maven Integration for Eclipse

Cytoscape build system has been moved to Maven. To use maven on Eclipse, you need to follow [:MavenInfo:this] instruction.

Now your Eclipse is ready for Cytoscape 3 development!

My Testing Environment

I tested the following tutorial in the following environment:

• RHEL 4 Workstation
• Java SE 5 update 15
• Eclipse 3.4 (32 bit version)

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.

1. Start Eclipse

2. Checkout Cytoscape 3 from the current SVN trunk. Set project type to Java Project and name the project (in this example, I'll use C3 as project name).

3. Quit Eclipse

4. From terminal, run mvn clean install pax:eclipse. This command automatically generates Eclipse project files. This process takes about 10 minutes to complete.

5. Start Eclipse again

6. Select File → Import and import as Maven Project

   • attachment:eclipse_core1.png

7. Select all pom files and press Finish. Your Eclipse workspace looks like the following image

   • attachment:eclipse_core2.png

Run Cytoscape 3 on Eclipse

Eclipse is running on an OSGi implementation called [http://www.eclipse.org/equinox/ Equinox]. Since Cytoscape 3 is following OSGi standard, (theoritically) you can run it on any OSGi environments. In this example, you will run Cytoscape 3 using Equinox.

1. From Eclipse main window, select Run → Run Configurations

2. Right click on OSGi Framework and select New

   • attachment:eclipse_core3.png

3. Name the configuration Cytoscape 3

4. By default, every bundle available in current Equinox environment is selected. Uncheck Target Platform bundles. At this point, only Cytoscape 3 bundles are selected.

5. Press Add Required Bundles button. This function automatically select required (infrastructure) bundles to run Cytoscape 3 bundles under Workspace

   • attachment:eclipse_core4.png

6. Press Run. After few moments, Cytoscape Desktop appears. In the console window, you can see the messages to standard output

   • attachment:eclipse_core5.png

osgi> ss

Framework is launched.

id      State       Bundle
0       ACTIVE      org.eclipse.osgi_3.4.0.v20080605-1900
                    Fragments=48
1       ACTIVE      com.sun.xml.bind.jaxb-xjc_2.0.0
2       ACTIVE      csplugins.quickfind_1.0.0.SNAPSHOT
3       ACTIVE      phoebe.dnd_1.0.0.SNAPSHOT
4       ACTIVE      org.freehep.swing_2.0.2
5       ACTIVE      org.eclipse.datatools.modelbase.sql.query_1.0.1.v200805152355
6       ACTIVE      net.sourceforge.lpg.lpgjavaruntime_1.1.0.v200803061910
7       ACTIVE      cytoscape.graph.dynamic_1.0.0.SNAPSHOT
8       RESOLVED    org.eclipse.core.runtime.compatibility.registry_3.2.200.v20080610
                    Master=31
9       ACTIVE      cytoscape.graph.fixed_1.0.0.SNAPSHOT
10      ACTIVE      cytoscape-temp.sbml2_1.0.0
11      ACTIVE      cytoscape.geom.rtree_1.0.0.SNAPSHOT
12      RESOLVED    org.eclipse.core.resources.compatibility_3.4.0.v20080604-1400
                    Master=77
13      ACTIVE      org.eclipse.ant.core_3.2.0.v20080529

Develop Cytoscape 3 Code on Eclipse PDE

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 build as a Maven project and has a pom.xml file.

Debugging Cytoscape 3 Code with Eclipse Debugger

Essentially, there is no difference between regular Java program debugging and OSGi system debugging. Eclipse built-in OSGi environment is integrated to other part of Eclipse, and you can use

(Under construction)

This document is written by Keiichiro Ono