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SBML export/import for CSG Geometry not working #423

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Tracked by #1036
jcschaff opened this issue Sep 28, 2022 · 1 comment · May be fixed by #424
Open
Tracked by #1036

SBML export/import for CSG Geometry not working #423

jcschaff opened this issue Sep 28, 2022 · 1 comment · May be fixed by #424

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@jcschaff
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SBML export/import for CSG Geometry not working. An NullPointerException exception is thrown when trying to round-trip to SBML with a CSG (Constructive Solid Geometry) geometry. (see biomodel_124562627.vcml)

After looking at the SBMLExporter and Importer, it is clear that the typical implementation within vcell (an analytic background subvolume with one or more CSG objects) is not supported at all.

The strategy is to translate the background into an oversized CUBE to form the "background" - so that all of the SubVolumes can be exported as CSGObjects (rather than a mixture of CSGObjects and AnalyticSubVolumes) and will translate well to SBML. The SBMLImporter likely needs some work as well with respect to CSG Geometries.

@jcschaff jcschaff added the VCell-7.5.0 Needed for Release 7.5 label Sep 28, 2022
@jcschaff jcschaff self-assigned this Sep 28, 2022
@jcschaff jcschaff moved this to In Progress in vcell development Sep 28, 2022
@jcschaff jcschaff linked a pull request Sep 28, 2022 that will close this issue
@jcschaff jcschaff linked a pull request Sep 28, 2022 that will close this issue
@jcschaff jcschaff added VCell-7.6.0 and removed VCell-7.5.0 Needed for Release 7.5 labels Oct 12, 2022
@moraru
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moraru commented Oct 31, 2022

This affects 3 simcontexts in published models and 16 simcontexts in public models

@CodeByDrescher CodeByDrescher added this to the Model Processing milestone Dec 20, 2022
@CodeByDrescher CodeByDrescher moved this from In Progress to Queued in vcell development Apr 25, 2023
@CodeByDrescher CodeByDrescher moved this from Queued to Pool in vcell development Oct 17, 2023
@jcschaff jcschaff moved this from Pool to Active in vcell development Nov 4, 2023
@jcschaff jcschaff removed this from the Model Processing milestone Nov 15, 2023
@jcschaff jcschaff moved this from Active to Queued in vcell development Nov 15, 2023
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