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neilswainston / SbmlToSbol

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AttributeError: 'NoneType' object has no attribute 'getGroup' #3

Open yzongy opened 2 years ago

yzongy commented 2 years ago

Hi Neil,

I am trying to convert the yeast genome-scale metabolic model to SBOL with the galaxy tool, but something went wrong there.

Is there any way to fix that?

Traceback (most recent call last): File "/galaxy/database/dependencies/_conda/envs/sbml2sbol@0.1.12/lib/python3.7/runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "/galaxy/database/dependencies/_conda/envs/sbml2sbol@0.1.12/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/galaxy/database/dependencies/_conda/envs/sbml2sbol@0.1.12/lib/python3.7/site-packages/sbml2sbol/main.py", line 25, in entry_point() File "/galaxy/database/dependencies/_conda/envs/sbml2sbol@0.1.12/lib/python3.7/site-packages/sbml2sbol/main.py", line 20, in entry_point uniprotID_key=args.uniprotID_key File "/galaxy/database/dependencies/_conda/envs/__sbml2sbol@0.1.12/lib/python3.7/site-packages/sbml2sbol/converter.py", line 77, in convert uniprotID_key=uniprotID_key File "/galaxy/database/dependencies/_conda/envs/__sbml2sbol@0.1.12/lib/python3.7/site-packages/sbml2sbol/converter.py", line 109, in _read_sbml rp_pathway = document.model.getPlugin('groups').getGroup(pathway_id) AttributeError: 'NoneType' object has no attribute 'getGroup'

breakthewall commented 2 years ago

Hi,

actually the tool is a little bit misnamed since it extracts UniProt IDs of enzymes that catalyze the reactions in an heterologous pathway stored in an enriched SBML format. And I guess this is not what you try to do.

Best regards, Joan