Find a robust way to call Java from python and start using OPSIN and OSCAR5 - Githubissues

chembl / curation-interface

This is repository to track all bugs and issues related to development of the curation interface

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Find a robust way to call Java from python and start using OPSIN and OSCAR5 #98

Open mnowotka opened 9 years ago

mnowotka commented 9 years ago

There are some important pieces of cheminformatics software written in Java that should be accessible fro our Python stack.

Currently I believe that the only robust way to join Java and Python together is to run two separate instances of python interpreter:

standard cython for running django and stuff
jython for calling java

The question is how to join those two python interpreters together. I see two possibilites:

use pyro4 library but there are some compatibility issues with jython.
use rabbitMQ to implement RPC.

Both methods should be investigated and finally we should have a robust connection. What we can implement then is:

PDF chemical entity recognition that is sent back to client and highlighted in the original PDF preview.
Mapping from compound records activities to their original occurrences highlighted in original PDF preview.