You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
~/.local/lib/python3.9/site-packages/mass/io/sbml.py in read_sbml_model(filename, f_replace, **kwargs)
537 doc = _get_doc_from_filename(filename)
--> 538 return _sbml_to_model(doc, f_replace=f_replace, **kwargs)
539
~/.local/lib/python3.9/site-packages/mass/io/sbml.py in _sbml_to_model(doc, f_replace, **kwargs)
675 # and GPR information.
--> 676 reactions, local_params, custom_rates = _read_model_reactions_from_sbml(
677 model, mass_model.metabolites, f_replace, **kwargs
~/.local/lib/python3.9/site-packages/mass/io/sbml.py in _read_model_reactions_from_sbml(model, metabolites, f_replace, **kwargs)
1292 mass_notes = _parse_notes_dict(reaction)
-> 1293 mass_reaction.gpr = _read_reaction_gpr_from_sbml(
1294 reaction, mass_notes, f_replace
~/.local/lib/python3.9/site-packages/cobra/core/reaction.py in gpr(self, value)
520 self._gpr = value
--> 521 self._update_genes_from_gpr()
522
~/.local/lib/python3.9/site-packages/cobra/core/reaction.py in _update_genes_from_gpr(self, new_gene_names)
429 if self._gpr is not None:
--> 430 new_gene_names = self._gpr.genes
431 else:
AttributeError: 'str' object has no attribute 'genes'
The above exception was the direct cause of the following exception:
MassSBMLError Traceback (most recent call last)
<ipython-input-2-1b0305e75d56> in <module>
----> 1 mass.io.sbml.read_sbml_model('../Biosimulators_test_suite/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism/WholeCellRBC_MA_Rates.xml')
~/.local/lib/python3.9/site-packages/mass/io/sbml.py in read_sbml_model(filename, f_replace, **kwargs)
553 "at https://github.com/SBRG/masspy/issues ."
554 )
--> 555 raise_from(mass_error, original_error)
556
557
/usr/local/lib/python3.9/dist-packages/six.py in raise_from(value, from_value)
MassSBMLError: Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
Environment
MASSpy 0.1.6
COBRA 0.24.0
The text was updated successfully, but these errors were encountered:
Steps to reproduce
Error
Environment
The text was updated successfully, but these errors were encountered: