SBML/COMBINE export with roundtrip validation

virtualcell / vcell

Virtual Cell Framework

http://vcell.org/

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SBML/COMBINE export with roundtrip validation #229

Closed jcschaff closed 2 years ago

jcschaff commented 2 years ago

The VcmlOmexConverter used in exporting SBML/SEDML (together in an .omex file - the COMBINE archive) did not verify that the resuting .omex file could be re-parsed by VCell. This round-tripping needs to be put in place to shorten the development cycle and fail an export which is invalid.

jcschaff commented 2 years ago

created branch and introduced:

introduced logging (using log4j2) to replace verbose print statements in SBML/SEDML import/export classes.
omex file validation by immediately re-reading the exported omex files to perform basic validation (omex file parse doesn't fail).
fixed SEDML export of "initCount" parameters (for stochastic VCell applications).
better error message for SBML export with membrane voltage.
fixed SBML import of 2D/3D geometries with respect to subvolumes and membranes.

jcschaff commented 2 years ago

Known Problem: In SBML import/export related to AssignmentRules variables not being imported or exported properly for diffusion coefficient. This will be fixed in a follow up issue.

jcschaff commented 2 years ago

see PR 230