[Jython-users] Re: [Jython-dev] A query regarding usage of Biopython Api in Jython compiled class ?

[Robert W. B. <rb...@di...>]

Note: moved to jython-users

On Fri, 23 Nov 2001, Bhavani wrote:
> Here I am making use of BioPython Api to fetch the Gene details
> thro NCBI Database server. If it is in Python environment it works
> fine. But If I convert that Python class to Java class using the
> Jython tool and try to run java (python) class it is throwing an
> exception

Disclaimer: I'm unqualified to comment on BioPython specifically.

I assume "Jython tool" means jythonc, and that "Python environment" means
running as a script with jython rather that with CPython. Is that right?
If so, it is likely just a bad/missing python.home when using the compiled
classes.

> Exception details are below:
> ---------------------------------------
> Error in GeneSearch
>
> Java Traceback:
>
>         at org.python.core.Py.ImportError(Py.java)
>         at org.python.core.imp.importFromAs(Compiled Code)
>         at org.python.core.imp.importFrom(imp.java)
>         at GeneSearch$_PyInner.main$4(GeneSearch.java:169)
>         at GeneSearch$_PyInner.call_function(GeneSearch.java:58)
>         at org.python.core.PyTableCode.call(Compiled Code)
>         at org.python.core.PyCode.call(PyCode.java)
>         at org.python.core.imp.createFromCode(imp.java)
>         at org.python.core.Py.initProxy(Compiled Code)
>         at GeneSearch.__initProxy__(GeneSearch.java:227)
>         at GeneSearch.<init>(GeneSearch.java:205)
>         at GeneSearchTest.main(Compiled Code)
> Traceback (innermost last):
>   File "D:\jython2.1\SampleProj\GeneSearch.py", line 0, in main
> ImportError: cannot import name GenBank

try printing your sys.path variable and the python.home property.  If they
are wrong, try setting python.home in the command line with Java's -D
switch (-Dpython.home=D:\jython2.1).

> ***** Here GenBank is present in Biopython API and is going to
>        installed seperately into python directory after installing python
>        I have installed the Biopython api in the Lib direcotry of python
>       and even updated the python.path to point to the respective
>       directory both in registry file of jython as well as the environmental
>       settings
>
> Can you suggest me what are other settings I have to make to
> make use of BioPython along with Jython

If you've compiled GeneSearch.py with jythonc without switches, try running
it with something like this:

java -Dpython.home=D:\jython2.1 -cp D:\jython2.1\jython.jar;. GeneSearch

alternatively, you can statically compile the script so that you there's no
need to rely on Jython's Lib.

jythonc --deep --jar gs.jar GeneSearch.py
java -cp gs.jar;D:\jython2.1\jython.jar GeneSearch

If this is not helpful, reply with following info:
    1. which jythonc switches you used
    2. add debug print statements to look at python.home and sys.path, and
       include their output in your reply:
       import sys, java
       print sys.path
       print java.lang.System.getProperty("python.home")

-robert