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Hi Andrew,

Sent again to the list because the attachment size was too large.

> The RDF containers library for the CellML API has now been pushed to the
> sourceforge repository, and in addition, I have now implemented a Java
> wrapper around the functionality for adding controlled vocabulary terms.
> I have aimed to make the wrapper as similar to the one from libSBML.

Thank you very much for writing this! I've been attempting to integrate
them into Saint for the past few days.

> The RDF containers library has proper unit tests. The CVTerm
> implementation does not - it may or may not actually work as it has
> never been tested (I expect it will change in response to feedback from
> Morgan and Allyson anyway).

Unfortunately, the CVTerm class crashes the JRE when it is instantiated.
I've narrowed the crash to the call to findOrMakeContainer in the lowest
level constructor, so it's a problem with the RDF containers library.

A test project is located at
http://dl.dropbox.com/u/4048178/CVTermTest.zip in Maven build format.
Please note the direct links in
src/test/java/cellml_api/CVTermTest.java - you'll have to modify them
appropriately. The files are located at /src/test/resources .

I'm not a C++ programmer, so unfortunately I have no idea what could be
causing the error. Here is the exact (scary-looking) error:

#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0xb6f82c96, pid=13117, tid=3065916272
#
# JRE version: 6.0_16-b01
# Java VM: Java HotSpot(TM) Server VM (14.2-b01 mixed mode linux-x86 )
# Problematic frame:
# V [libjvm.so+0x379c96]
#
# An error report file with more information is saved as:
# /home/morgan/Development/CellML/CVTermTest/hs_err_pid13117.log
#
# If you would like to submit a bug report, please visit:
# http:/java.sun.com/ebapps/ugreport/rash.jsp
#

The error report is also attached. I'm using the most recent CellML API
version changeset 919:8f6038db67a7, installed to Maven using:

mvn install:install-file -DgroupId=org.cellml -DartifactId=libcellml
-Dversion=1.6 -Dpackaging=jar -Dfile=cellml.jar

Aside from the error, everything for adding annotation looks good. I've
written most of the code for that now and it's only a matter of debugging.

However, although we can add annotation to CellML files now, we have no
way of querying what existing annotation exists on the model or element.
We would need this when loading in models that have already been
partially annotated, or for adding more annotation to previously
annotated models. If you want to stick with this CVTerm being outside
the API, we would suggest a method with a signature along the following
lines:

public static List<CVTerm> getCVTerms(CellMLElement element);

where it will query the RDF in the model for the CellMLElement and
return a list consisting of new (read-only) CVTerms. I hope that won't
be too difficult?

> (I get
> failures later on compiling GWT, but that seems to be an entirely
> different issue).

Thanks for pointing it out. It was a GWT versioning issue and has been
fixed. :)

We're very excited to be able to proceed with this. I hope you have a
nice weekend, and we look forward to hearing from you soon.

Cheers,
Morgan and Allyson
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• [cellml-dev] Java CVTerm implementation, Andrew Miller, 04/07/2010
  • [cellml-dev] Java CVTerm implementation, Morgan Taschuk, 04/10/2010
  • Message not available
    • [cellml-dev] Java CVTerm implementation, Andrew Miller, 04/14/2010
      • [cellml-dev] Java CVTerm implementation, Morgan Taschuk, 04/15/2010
        • [cellml-dev] Java CVTerm implementation, Andrew Miller, 04/15/2010
          • [cellml-dev] Java CVTerm implementation, Morgan Taschuk, 04/16/2010
            • [cellml-dev] Java CVTerm implementation, David Nickerson, 04/16/2010
              • [cellml-dev] Java CVTerm implementation, Andrew Miller, 04/16/2010
              • [cellml-dev] Java CVTerm implementation, David Nickerson, 04/16/2010
            • [cellml-dev] Java CVTerm implementation, Andrew Miller, 04/16/2010

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