sbmlutils
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Ensure sbmlinfo is working on model import
The models created with "SBML -> Model -> SBML -> SBMLInfo" must be valid. Currently issues with the new ModelEquation:
An error occurred. Please report this on
https://github.com/matthiaskoenig/sbmlutils/issues/new
so we can improve the service.
{
"errors": [
"Half equation could not be generated: '<SpeciesReference>'",
"Traceback (most recent call last):\n File \"/code/src/sbmlutils/report/api.py\", line 122, in report_from_file\n return json_for_omex(path)\n File \"/code/src/sbmlutils/report/api.py\", line 192, in json_for_omex\n content[\"reports\"][entry.location] = json_for_sbml( # type: ignore\n File \"/code/src/sbmlutils/report/api.py\", line 209, in json_for_sbml\n info = SBMLDocumentInfo.from_sbml(source=source)\n File \"/code/src/sbmlutils/report/sbmlinfo.py\", line 61, in from_sbml\n return SBMLDocumentInfo(doc=doc)\n File \"/code/src/sbmlutils/report/sbmlinfo.py\", line 55, in __init__\n self.info = self.create_info()\n File \"/code/src/sbmlutils/report/sbmlinfo.py\", line 83, in create_info\n model = self.model_dict(self.doc.getModel())\n File \"/code/src/sbmlutils/report/sbmlinfo.py\", line 122, in model_dict\n \"reactions\": self.reactions(model=model),\n File \"/code/src/sbmlutils/report/sbmlinfo.py\", line 849, in reactions\n d[\"equation\"] = self._equation_from_reaction(r)\n File \"/code/src/sbmlutils/report/sbmlinfo.py\", line 988, in _equation_from_reaction\n left = SBMLDocumentInfo._half_equation(reaction.getListOfReactants())\n File \"/code/src/sbmlutils/report/sbmlinfo.py\", line 1036, in _half_equation\n raise ValueError(f\"Half equation could not be generated: '{sr}'\")\nValueError: Half equation could not be generated: '<SpeciesReference>'\n"
],
"warnings": [],
"info": {}
}