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tellurium handles some SED-ML mathematical expressions incorrectly #521

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jonrkarr opened this issue Apr 21, 2021 · 0 comments
Open

tellurium handles some SED-ML mathematical expressions incorrectly #521

jonrkarr opened this issue Apr 21, 2021 · 0 comments

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@jonrkarr
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from the L1V3/L1V3_oscli-nested-pulse.omex example in the sed-ml.io repo

    factory.executePython()
  File "/usr/local/lib/python3.7/site-packages/tellurium/sedml/tesedml.py", line 510, in executePython
    code = self.toPython()
  File "/usr/local/lib/python3.7/site-packages/tellurium/sedml/tesedml.py", line 497, in toPython
    pysedml = template.render(c)
  File "/usr/local/lib/python3.7/site-packages/jinja2/environment.py", line 1090, in render
    self.environment.handle_exception()
  File "/usr/local/lib/python3.7/site-packages/jinja2/environment.py", line 832, in handle_exception
    reraise(*rewrite_traceback_stack(source=source))
  File "/usr/local/lib/python3.7/site-packages/jinja2/_compat.py", line 28, in reraise
    raise value.with_traceback(tb)
  File "/usr/local/lib/python3.7/site-packages/tellurium/sedml/templates/tesedml_template.template", line 62, in top-level template code
    {{ taskToPython(doc, task) }}
  File "/usr/local/lib/python3.7/site-packages/tellurium/sedml/tesedml.py", line 697, in taskToPython
    return SEDMLCodeFactory.taskTreeToPython(doc, tree=taskTree)
  File "/usr/local/lib/python3.7/site-packages/tellurium/sedml/tesedml.py", line 808, in taskTreeToPython
    taskLines = SEDMLCodeFactory.repeatedTaskToPython(doc, node=node)
  File "/usr/local/lib/python3.7/site-packages/tellurium/sedml/tesedml.py", line 1207, in repeatedTaskToPython
    value = evaluableMathML(r.getMath(), variables=variables)
  File "/usr/local/lib/python3.7/site-packages/tellurium/sedml/mathml.py", line 113, in evaluableMathML
    astnode.replaceArgument(key, libsbml.parseFormula(str(value)))
AttributeError: 'NoneType' object has no attribute 'replaceArgument'
@jonrkarr jonrkarr changed the title tellurium handles some formulas incorrectly tellurium handles some SED-ML mathematical expressions incorrectly Apr 21, 2021
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