Cannot read archive with python bindings

[matthiaskoenig]

Hi all, I am trying to read combine archives via the python bindings, but always get errors about empty XML content when trying to read the archives. I am not sure what I am doing wrong

from __future__ import print_function, division
import libcombine

def get_content(path):
    print(path)
    # libsbml.readSBMLFromFile(path)
    manifest = libcombine.readOMEXFromFile(str(path))

    print("Errors:", manifest.getNumErrors())
    for k in xrange(manifest.getNumErrors()):
        error = manifest.getError(k)
        print(error)
        print(error.getErrorId())
        print(error.getMessage())

    # make CaListOfContents iteratable
    contentsList = manifest.getListOfContents()
    print('Contents: ', contentsList.getNumContents())
    for k in xrange(contentsList.getNumContents()):
        cabase = contentsList.get(k)
        print(cabase)

    print(manifest)

if __name__ == "__main__":
    """
    Try to read the showcase archive.
    """
    archive = "CombineArchiveShowCase.omex"
    get_content(archive)

Archive is the CombineArchiveShowCase from http://scripts.sems.uni-rostock.de/getshowcase.php

Errors are:

/usr/bin/python2.7 /home/mkoenig/git/tellurium-web/teweb/combine/oven/libcombine_example.py
CombineArchiveShowCase.omex
Errors: 2
<libcombine.CaError; proxy of <Swig Object of type 'CaError_t *' at 0x7effbde5d300> >
1035
Main XML content is empty.

<libcombine.CaError; proxy of <Swig Object of type 'CaError_t *' at 0x7effbde5d330> >
1002
Missing encoding attribute in XML declaration.

Contents:  0
<libcombine.CaOmexManifest; proxy of <Swig Object of type 'CaOmexManifest_t *' at 0x7effbfc77f90> >

Process finished with exit code 0

[fbergmann]

Hello Matthias,

the readOMEX functions are just there to read the manifest file. All the zip logic and other stuff is in the CombineArchive class as written in the release announcement. If you want just to read the archive, please have a look at the print example:

https://github.com/sbmlteam/libCombine/blob/master/examples/python/printExample.py

or if you would like to create one you could use the create example:

https://github.com/sbmlteam/libCombine/blob/master/examples/python/createArchiveExample.py

we also have rudimentary documentation of the combinearchive class available here:

https://sbmlteam.github.io/libCombine/html/class_combine_archive.html

best Frank

[matthiaskoenig]

Perfect. Thanks a lot this makes everything clear.