~+'''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 [[http://networkx.sourceforge.net/|NetworkX]]

Anyone with experience in this topic?