Fix SBML Rule handling logic #120
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RateRules were ignored so far...
dilpath
approved these changes
Apr 4, 2022
Comment on lines
412
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+418
| if not with_values: | ||
| return [p.getId() for p in sbml_model.getListOfParameters() | ||
| if sbml_model.getAssignmentRuleByVariable(p.getId()) is None] | ||
| if sbml_model.getRuleByVariable(p.getId()) is None] | ||
|
|
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| return {p.getId(): p.getValue() | ||
| for p in sbml_model.getListOfParameters() | ||
| if sbml_model.getAssignmentRuleByVariable(p.getId()) is None} | ||
| if sbml_model.getRuleByVariable(p.getId()) is None} |
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Just some duplicated code, fine as is.
Suggested change
| if not with_values: | |
| return [p.getId() for p in sbml_model.getListOfParameters() | |
| if sbml_model.getAssignmentRuleByVariable(p.getId()) is None] | |
| if sbml_model.getRuleByVariable(p.getId()) is None] | |
| return {p.getId(): p.getValue() | |
| for p in sbml_model.getListOfParameters() | |
| if sbml_model.getAssignmentRuleByVariable(p.getId()) is None} | |
| if sbml_model.getRuleByVariable(p.getId()) is None} | |
| parameters = { | |
| p.getId(): p.getValue() | |
| for p in sbml_model.getListOfParameters() | |
| if sbml_model.getRuleByVariable(p.getId()) is None | |
| } | |
| if not with_values: | |
| return list(parameters.keys()) | |
| return parameters |
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You are right about the duplication, but I'd still keep it as is. For large models, this saves quite a couple of XML lookups.
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RateRules were ignored so far...
Related to PEtab-dev/PEtab#539, PEtab-dev/PEtab#513