search

ISA-tools / mzml2isa

Parser to get meta information from mzML file and parse relevant information to a ISA-Tab structure
GNU General Public License v3.0
12 stars 6 forks source link

[1.1.0] - import mzml2isa - ValueError: could not find `owl:Ontology` element #49

Closed DrYak closed 1 year ago

DrYak commented 1 year ago

The import mzml2isa test of the bioconda package for the auto bumped version 1.1.0 is currently failing with an error message :

09:16:47 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/mzml2isa_1665911628804/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/python3.9/site-packages/pronto/parsers/rdfxml.py", line 89, in parse_from
09:16:47 BIOCONDA INFO (OUT)     raise ValueError("could not find `owl:Ontology` element")
09:16:47 BIOCONDA INFO (OUT) ValueError: could not find `owl:Ontology` element

Is there something wrong?

DrYak commented 1 year ago

Culprit seems to be here:

09:16:47 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/mzml2isa_1665911628804/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/python3.9/site-packages/mzml2isa/mzml.py", line 64, in <module>
09:16:47 BIOCONDA INFO (OUT)     class MzMLFile(object):
09:16:47 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/mzml2isa_1665911628804/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/python3.9/site-packages/mzml2isa/mzml.py", line 105, in MzMLFile
09:16:47 BIOCONDA INFO (OUT)     _VOCABULARY = pronto.Ontology(filename)

(BTW, same error message as that pronto issue)

althonos commented 1 year ago

This issue is raised when pronto fails to load an XML document, which happens typically when trying to resolve a missing ontology on http://purl.obolibrary.org, which may return an XML listing (that's a bug in itself). I just noticed that stato.owl was not embedded as expected in the mzml2isa distribution, so it's likely that pronto was trying to find it online and failed. I'll make a new release fix the missing file included.

althonos commented 1 year ago

Looks like the issue is fixed in v1.1.1, the Bioconda build is fine. :+1: