CCopasiException on invalid archive about biosimulators_copasi HOT 5 CLOSED

For reference:

BIOMD0000000793.omex.zip

from biosimulators_copasi.

If this is always an issue for the COPASI Python interface, the command line program will need to be implemented differently or COPASI will need to fix the problem.

This won't crash the main BioSimulations application because the simulation jobs will be run on the cluster. We realized that some jobs would not complete successfully, and plan to store the stdout and stderr logs. This is already part of the BioSimulations data model.

from biosimulators_copasi.

I'll have a look at this, in general though, it would be great if you could file issues like that on our issue tracker, so we know about them and can resolve them. I've done this now, and will track it there.

http://tracker.copasi.org/show_bug.cgi?id=2908

from biosimulators_copasi.

This is just to let you know that this has been resolved in the current python-copasi package on pypi (and any version > 4.29.227 will do). Now you will still get the exception, but you could handle it if you so choose:

import COPASI
dm = COPASI.CRootContainer.addDatamodel()
try:
  dm.openCombineArchive('BIOMD0000000793.omex')
except COPASI.CCopasiException as e:
  print(e.getMessage().getText())

which for your model would give you something like:

>EXCEPTION 2020-08-11T08:40:52<
  SEDML (4): Could not open file "/tmp/copasi/fbergmann/q8fkec53/Chen2011/1.xml". Note: The reference SBML model in SEDML document must be saved in the same directory as the SEDML document using the source attribute value as the file name .

from biosimulators_copasi.

In my testing, this is fixed. Thanks @fbergmann!

from biosimulators_copasi.