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PEtab-dev / PEtab

PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
https://petab.readthedocs.io
MIT License
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Extend validator to check if all required parameters are present in parameter table #43

Closed dweindl closed 4 years ago

dweindl commented 5 years ago

See #42 for what to check.

Should be added to petab/lint.py:

def check_parameter_sheet(problem):

EDIT: Also check that there are no additional parameters

elbaraim commented 5 years ago

do we want to also check this with the SBML model? Meaning that all parameters defined in the SBML are present in the parameter sheet?

dweindl commented 5 years ago

All besides the ones appearing as column names in the condition table, yes.

dweindl commented 5 years ago

Added first part. Check for parameter overrides from measurement table still missing.

erikadudki commented 5 years ago

@dweindl has this been addressed sufficiently?

dweindl commented 5 years ago

@dweindl has this been addressed sufficiently?

No, at least not by me or by any commit referencing this issue. What needs to be checked here is that all parameters introduced in the condition table (as value, not column - i.e. parameter overrides) are present in the parameter table.

dweindl commented 4 years ago

See also https://github.com/LeonardSchmiester/Benchmark-Models/issues/4#issuecomment-559496231. This is not sufficiently checked yet