integrating python script with Java application

[systemsbiology]

Hello Everyone,

I am an intermediate developer in programming languages. I have developed some python script and some java applications. In my project, I need to integrate the python script with a java application to put all the tools in a single pipeline to function as a continuous workflow.

This python script and the java program are completely developed and can work as independent modules in the pipeline. The output of the Python script is a text file which should be read by the java application as an input.

I read about Jython, SWIG & JPype. Can anyone direct/advice me in choosing the effective approach to integrate my applications,other than the command line(CL) invocation.

Jython is slower than Python. Hence, I am hesitant to use Jython as top layer program which can call the python script and the java application sequentially.

And SWIG is for the integration of C/C++ Applications with scripting languages like python/perl and also with java

I would like to appreciate you for reading this posting. Please give me some advice.

Thank you,

[Stefano Mtangoo]

You seem to be finding something like Jython
Jython is Python implementation of Java. I dont know Java so... I haven't looked Jython
www.jython.org

[~s.o.s~]

> I need to integrate the python script with a java application to put
> all the tools in a single pipeline to function as a continuous workflow

There are a few things I can think of:
- If only one component of the workflow executes at a given time and if the execution of component `n' commences only after the execution of component `n - 1', you can simply create a shell script which sequentially executes the processes. Something like:

python some.py | java pkg.class | java otherpkg.otherclass

But this approach is crude and might not work if there are other complications involved.

- Instead of a Jython wrapper, create a pure Java wrapper which initiates and executes the entire workflow. You can try embedding the Python interpreter to execute your Python scripts from Java.

- Don't believe the FUD floating around about Jython being slow; try it for your application and see if it works out within the given expectations. Using a recent JVM [1.6] and the latest Jython build might help speed things up.

[adamghering]

I just want to be pointed in the right direction. I am new to java but know enough python to get myself into trouble. I am writing some scripts that work with a program and so it has to be in java. I was wondering though. can't I just initiate a java script that then runs a more streamlined python script and then returns to the java...?

any advice?

[~s.o.s~]

As already mentioned, look into the embedding jython section for more details, esp the usage of ScriptEngine API to invoke external scripts.

In case you are still facing problems, I'd recommend hitting the jython mailing list/forum for quick answers.