Using a java library from python
Wrap your Java-Code in a Container    (Servlet / EJB). 
So you don´t loose time in the vm-startup and you go the way to more service-oriented. 
For the wraping you can use jython (only make sense if you are familiar with python)
Choose a    communication-protocoll in which python and java can use:

json (see  www.json.org)   
rmi (Python: JPype)
REST
SOAP (only for the brave)

Choose something you or your partners are familliar with!
I have a python app and java app. The python app generates input for the java app and invokes it on the command line.
I'm sure there must be a more elegant solution to this; just like using JNI to invoke C code from Java.
Any pointers?
(FYI I'm v. new to Python)  
Clarification (at the cost of a long question: apologies)
The py app (which I don't own) takes user input in the form of a number of configuration files. It then interprits these and farms work off to a number of (hidden) tools via a plugin mechanism. I'm looking to add support for the functionality provided by the legacy Java app.
So it doesn't make sense to call the python app from the java app and I can't run the py app in a jython environment (on the JVM).
Since there is no obvious mechanism for this I think the simple CL invocation is the best solution.