PluginsWithJython

How one can create Cytoscape plugins using Jython?

I (MarcioSilva) found at Cytoscape CVS the following file:

csplugins/isb/dtenenbaum/jython/doc/jython_and_java_web_start.txt

from Dan Tenenbaum, explaining how to run Jython plugins using Java Web Start.

I tried to follow the directions from the document above, but then I have the following files:

• PyConsolePlugin.jar (I am not sure I created this one right -- anyone can give some directions here?)

• jython.jar

• jython-lib.jar

• scripts.jar (this one has some python files and the __run__.py)

My question is: what should I do with this .jar files?

I tried to put all of them in the plugins/ folder of cytoscape, but then I have this error:

Exception in thread "main" java.lang.NoClassDefFoundError:
javax/servlet/http/HttpServlet
       at java.lang.ClassLoader.defineClass0(Native Method)
       at java.lang.ClassLoader.defineClass(ClassLoader.java:539)
       at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:123)
       at java.net.URLClassLoader.defineClass(URLClassLoader.java:251)
       at java.net.URLClassLoader.access$100(URLClassLoader.java:55)
       at java.net.URLClassLoader$1.run(URLClassLoader.java:194)
       at java.security.AccessController.doPrivileged(Native Method)
       at java.net.URLClassLoader.findClass(URLClassLoader.java:187)
       at java.lang.ClassLoader.loadClass(ClassLoader.java:289)
       at java.lang.ClassLoader.loadClass(ClassLoader.java:235)
       at cytoscape.CytoscapeInit.isClassPlugin(CytoscapeInit.java:659)
       at cytoscape.CytoscapeInit.loadPlugins(CytoscapeInit.java:584)
       at cytoscape.CytoscapeInit.init(CytoscapeInit.java:207)
       at cytoscape.CyMain.<init>(CyMain.java:94)
       at cytoscape.CyMain.main(CyMain.java:166)

This seems to happen when Cytoscape tries to load jython.jar (because I removed PyConsolePlugin.jar from there and the same error happened -- when I removed jython.jar Cytoscape loaded normally).

Another question: in that document Dan mentions a file called:

org/python/core/SyspathArchiveHack.java

Where can I get it? And how to add it to the jython.jar (It is ok just do a jar xf add the file and jar cf again?).

I just want to make some plugins for Cytoscape using Jython. The reason is that I want to use some Python tools like NetworkX

Anyone with experience in this topic?