SBML export for parameter overrides

[vcellmike]

Any published model that has parameters override will give NullPointer Exception Dreyer 2022, Martin 2021, Rosenbloom 2021 RuntimeException-Could not apply overrides from simulation to application parameters : null NullPointerException-

King2021 - this model actually has an error in the database RuntimeException-Unable to perform operation. Errors found: The Simulation 'Uptake_Larger Jumps' has unused Math Overrides. See the Problems panel for a full list of errors and detailed error information.

[danv61]

"Dreyer 2022" biomodel_225440511 This is the correct message when we export to omex - model has electric

RuntimeException-Error adding model to SEDML document : SimContext 'Application0' could not be exported to SBML :Membrane 'PM has membrane potential enabled, SBML Export is not supported
Exception-SimContext 'Application0' could not be exported to SBML :Membrane 'PM has membrane potential enabled, SBML Export is not supported
UnsupportedSbmlExportException-Membrane 'PM has membrane potential enabled, SBML Export is not supported

[danv61]

When exporting to SBML:

RuntimeException-Could not apply overrides from simulation to application parameters : null
NullPointerException-

[jcschaff]

@vcellmike @moraru @danv61 what do we do about applying math overrides during SBML export when the selected Simulation has scanned parameters. Options are:

• skip scanned parameters
• fail with message
• filter those simulations
• enumerate parameter values over scan and choose median value for each parameter

Any ideas?

[jcschaff]

and if there are function dependencies in the parameter, e.g. default = 2.0, actual = (0.06667 * kon), then thinking it would make sense to only apply the numerical values rather than trying to introduce the functional dependency (complex and error prone).

[jcschaff]

regarding scanned parameters, will reproduce existing behavior of specifying the job index for each transform and exporting one SBML document per job.