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653 multiple spatial validation errors #655

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Merged
jcschaff merged 5 commits into from
Dec 7, 2022
Merged

653 multiple spatial validation errors #655

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51089bf
sbml spatial size not set is graceful (no confusing error messages).
jcschaff Dec 7, 2022
d1f0ec2
BioModel.updateAll(true) fixes spatial Unit Sizes, not just nonspatial
jcschaff Dec 7, 2022
608f2b6
Omex export in GUI calls BioModel.updateAll(true) to fix size mappings.
jcschaff Dec 7, 2022
ee94f0f
revert invocation of BioModel.updateAll(true) in Omex export from GUI.
jcschaff Dec 7, 2022
2a6d05a
solve for missing Unit Sizes during SBMLExport
jcschaff Dec 7, 2022
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5 changes: 5 additions & 0 deletions vcell-core/src/main/java/cbit/vcell/mapping/SimulationContext.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3792,6 +3792,11 @@ public void updateAll(boolean bForceUpgrade) throws MappingException {
double structSize = 1.0;
StructureSizeSolver.updateAbsoluteStructureSizes_symbolic(this, struct, structSize, struct.getStructureSize().getUnitDefinition());
}
if (getGeometry().getDimension() > 0 && !gc.isAllUnitSizeParameterSetForSpatial()) {
for (GeometryClass geometryClass : getGeometry().getGeometryClasses()) {
StructureSizeSolver.updateUnitStructureSizes(this, geometryClass);
}
}
}

//
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14 changes: 12 additions & 2 deletions vcell-core/src/main/java/org/vcell/sbml/vcell/SBMLExporter.java
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Expand Up @@ -271,8 +271,8 @@ private static boolean validSpatial(SimulationContext ctx) {
private void addCompartments() throws XMLStreamException, SbmlException {
Model vcModel = vcBioModel.getModel();
try {
// old vcell spatial application, with only relative compartment sizes (SBML wants absolute sizes for nonspatial ... easier to understand anyway)
if (!getSelectedSimContext().getGeometryContext().isAllSizeSpecifiedPositive() && getSelectedSimContext().getGeometry().getDimension() == 0) {
// old vcell nonspatial application, with only relative compartment sizes (SBML wants absolute sizes for nonspatial ... easier to understand anyway)
if (getSelectedSimContext().getGeometry().getDimension() == 0 && !getSelectedSimContext().getGeometryContext().isAllSizeSpecifiedPositive()) {
Structure structure = getSelectedSimContext().getModel().getStructure(0);
double structureSize = 1.0;
StructureMapping structMapping = getSelectedSimContext().getGeometryContext().getStructureMapping(structure);
Expand All @@ -281,6 +281,16 @@ private void addCompartments() throws XMLStreamException, SbmlException {
}catch (Exception e) {
throw new RuntimeException("Failed to solve for absolute compartment sizes for nonspatial application: "+e.getMessage(), e);
}
try {
// old vcell spatial application, with only relative compartment sizes (SBML wants absolute sizes for nonspatial ... easier to understand anyway)
if (getSelectedSimContext().getGeometry().getDimension() > 0 && !getSelectedSimContext().getGeometryContext().isAllUnitSizeParameterSetForSpatial()) {
for (GeometryClass geometryClass : getSelectedSimContext().getGeometry().getGeometryClasses()) {
StructureSizeSolver.updateUnitStructureSizes(getSelectedSimContext(), geometryClass);
}
}
}catch (Exception e) {
throw new RuntimeException("Failed to solve for unit sizes for spatial application: "+e.getMessage(), e);
}
cbit.vcell.model.Structure[] vcStructures = vcModel.getStructures();
for (int i = 0; i < vcStructures.length; i++) { // first we populate compartment vcell name to sbml id map
Compartment sbmlCompartment = sbmlModel.createCompartment();
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21 changes: 16 additions & 5 deletions vcell-core/src/main/java/org/vcell/sbml/vcell/SBMLImporter.java
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Expand Up @@ -4152,26 +4152,37 @@ private static void addGeometry(org.sbml.jsbml.Model sbmlModel, BioModel vcBioMo
Structure struct = ci.get();
String domainType = compMapping.getDomainType();
GeometryClass geometryClass = vcGeometry.getGeometryClass(domainType);
double unitSize = compMapping.getUnitSize();
Feature feat = BeanUtils.downcast(Feature.class,struct);
if (feat != null) {
FeatureMapping featureMapping = new FeatureMapping(feat, vcBioModel.getSimulationContext(0), vcModelUnitSystem);
featureMapping.setGeometryClass(geometryClass);
if (geometryClass instanceof SubVolume) {
featureMapping.getVolumePerUnitVolumeParameter().setExpression(new Expression(unitSize));
if (compMapping.isSetUnitSize()) {
double unitSize = compMapping.getUnitSize();
featureMapping.getVolumePerUnitVolumeParameter().setExpression(new Expression(unitSize));
}
sbmlSymbolMapping.putInitial(compMapping, featureMapping.getVolumePerUnitVolumeParameter());
} else if (geometryClass instanceof SurfaceClass) {
featureMapping.getVolumePerUnitAreaParameter().setExpression(new Expression(unitSize));
if (compMapping.isSetUnitSize()) {
double unitSize = compMapping.getUnitSize();
featureMapping.getVolumePerUnitAreaParameter().setExpression(new Expression(unitSize));
}
sbmlSymbolMapping.putInitial(compMapping, featureMapping.getVolumePerUnitAreaParameter());
}
structMappingsVector.add(featureMapping);
} else if (struct instanceof Membrane) {
MembraneMapping membraneMapping = new MembraneMapping( (Membrane) struct, vcBioModel.getSimulationContext(0), vcModelUnitSystem); membraneMapping.setGeometryClass(geometryClass);
if (geometryClass instanceof SubVolume) {
membraneMapping.getAreaPerUnitVolumeParameter().setExpression(new Expression(unitSize));
if (compMapping.isSetUnitSize()) {
double unitSize = compMapping.getUnitSize();
membraneMapping.getAreaPerUnitVolumeParameter().setExpression(new Expression(unitSize));
}
sbmlSymbolMapping.putInitial(compMapping, membraneMapping.getAreaPerUnitVolumeParameter());
} else if (geometryClass instanceof SurfaceClass) {
membraneMapping.getAreaPerUnitAreaParameter().setExpression(new Expression(unitSize));
if (compMapping.isSetUnitSize()) {
double unitSize = compMapping.getUnitSize();
membraneMapping.getAreaPerUnitAreaParameter().setExpression(new Expression(unitSize));
}
sbmlSymbolMapping.putInitial(compMapping, membraneMapping.getAreaPerUnitAreaParameter());
}
structMappingsVector.add(membraneMapping);
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