Ok, I will try this. Thanks a lot for your help! On Tue, May 11, 2010 at 7:50 PM, Christopher Schultz < ch...@christopherschultz.net> wrote:
> -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Silvio, > > On 5/11/2010 1:09 PM, Silvio Tschapke wrote: > > On 5/11/2010 11:36 AM, Silvio Tschapke wrote: > >>>> how do I configure tomcat that it finds the biopython libaries? > >>>> Biopython is not included in jython.jar (which I have moved into the > >>>> tomcat/lib folder. > >> > >> You probably want this JAR file in your webapp's WEB-INF/lib directory, > >> rather than in Tomcat's global lib directory. > >> > >>>> Biopython installs itself into the python26/lib/side-packages folder. > >> > >> Okay, what files does it put in there? > >> > >> > > There is no jar file. In the side-packages folder it puts a root folder > Bio > > which includes further folders with .py, .pyo, pyc files. > > Okay, those are Python scripts, compiled/optimized scripts, and compiled > scripts. Nothing in there is directly executable, so you probably don't > need to mess with your java.library.path setting. > > > I don't understand this. Do I have to tell Tomcat in a configuration file > > where it has to search for python or the libraries? > > Biopython works fine with Python outside my webserver. I am not sure if > it > > works with Jython too. But I thought that Jython works fine with Python > and > > Biopython is a subpackage so there shouldn'b be any problem. But I am not > > sure. > > You might want to read a bit more about Jython: it does not give you > access to the python environment on the local machine. Instead, it is > its own environment. Consider reading > http://www.jython.org/docs/tutorial/indexprogress.html > > If "Bio" uses direct C-library calls instead of Python functions, you're > out of luck for the time being. > > Your first step would be to determine if Bio will work with Jython: I > recommend getting in touch with the Jython folks to help you figure out > how to get Bio working with Jython. After that's working, it shouldn't > be difficult to move everything into Tomcat. > > >> Traceback (most recent call last): > >> File "C:/Documents and Settings/silvio/My > >> > Documents/eclipse_jee_workspace/Test_jee_with_jython/src/jyimplementation/Calculator.py", > >> line 2, in <module> > >> from Bio import Entrez > >> ImportError: No module named Bio > > > >> org.python.core.PyException.fillInStackTrace(PyException.java:70) > > So, somewhere there must be a place where you can configure where Jython > looks for modules. > > [...] > > >> > org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:190) > >> factory.JythonFactory.getJythonObject(JythonFactory.java:21) > >> main.Main.forwardRequest(Main.java:17) > > It looks like before you call execfile(), you might want to make some > other calls on either the PythonInterpreter object, or the PySystemState > object it's using, which seems to have something to do with locating > modules. > > >> servlets.MyServlet.doGet(MyServlet.java:36) > >> javax.servlet.http.HttpServlet.service(HttpServlet.java:617) > >> javax.servlet.http.HttpServlet.service(HttpServlet.java:717) > > > > > >> If I change the import command in my jython module from "from Bio import > >> Entrez" to "import Bio.Entrez" it doesn't work neither. > > > > > >> By the way..what means CNFE? :) > > That's ClassNotFoundException, which is a Java exception. You're not > getting that exception, but a different one from the Python interpreter. > Don't worry: you gave me what I was looking for. > > So, it just looks like you need to figure out how to tell Jython that > the Bio libraries are under .../lib/side-packages. I think you're going > to have to ask the Jython folks. > > Good luck, > - -chris > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.10 (MingW32) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iEYEARECAAYFAkvpmNsACgkQ9CaO5/Lv0PAESQCcC4gjP3G9QUM5L7hAnmb1iPlg > yOQAnjI8fXrcGPUyl+QJm/DUaf1ocbp+ > =v3t/ > -----END PGP SIGNATURE----- > > --------------------------------------------------------------------- > To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org > For additional commands, e-mail: users-h...@tomcat.apache.org > >
