When moving from 0.4.28 to 0.5.1, wrapper.py run produces an error when using test data.

Hi there!

We recently moved our container from 0.4.28 to 0.5.1 version of mzml2isa, only by changing the version used in pip install (see commit). When running wrapper.py with the test data available in this repo, it now fails like this:

/usr/local/lib/python2.7/dist-packages/mzml2isa/utils.py:267: UserWarning: Could not use latest online MS ontology, using local (version [u'4.0.1'])
  "using local (version {})".format(obo.meta['version']))
/usr/local/lib/python2.7/dist-packages/mzml2isa/utils.py:274: UserWarning: Could not use latest online IMS ontology, using local (version [u'0.9.1'])
  "using local (version {})".format(obo.meta['version']))
Traceback (most recent call last):
  File "/usr/local/bin/wrapper.py", line 235, in <module>
    main()
  File "/usr/local/bin/wrapper.py", line 215, in main
    multip=False)
  File "/usr/local/lib/python2.7/dist-packages/mzml2isa/parsing.py", line 231, in full_parse
    convert(*args, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/mzml2isa/parsing.py", line 121, in convert
    meta_loader = UserMetaLoader(kwargs.get('usermeta', None))
  File "/usr/local/lib/python2.7/dist-packages/mzml2isa/usermeta.py", line 322, in __init__
    elif usermeta_token.endswith('.xlsx'):
AttributeError: 'dict' object has no attribute 'endswith'

Commands invoked for testing are here. Any suggestions?

Thanks! Pablo

ISA-tools / mzml2isa-galaxy

When moving from 0.4.28 to 0.5.1, wrapper.py run produces an error when using test data. #6