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#275: check that spatial dimensions match before running test #276

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merged 5 commits into from
Oct 28, 2022
Merged

#275: check that spatial dimensions match before running test #276

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9e41596
#275: check that spatial dimensions match before running test
fbergmann Oct 27, 2022
09566fc
- compare spatial dimensions of other domain's compartment
fbergmann Oct 27, 2022
57a414a
Change the validation message to match.
luciansmith Oct 27, 2022
d8e8e0b
'must'->'should'.
luciansmith Oct 27, 2022
4733698
Also apply caveat to 21351.
luciansmith Oct 27, 2022
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8 changes: 4 additions & 4 deletions src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
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Original file line number Diff line number Diff line change
Expand Up @@ -882,9 +882,9 @@ static const packageErrorTableEntry spatialErrorTable[] =
{ SpatialCompartmentMappingUnitSizeMustBeFraction,
"The 'unitSize' attribute must be between 0 and 1.",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
"The attribute 'spatial:unitSize' on a <compartmentMapping> must have a value "
"between 0 and 1, inclusive.",
LIBSBML_SEV_WARNING,
"The attribute 'spatial:unitSize' on a <compartmentMapping> should have a value "
"between 0 and 1, inclusive, when the dimensions of the referenced compartments are the same.",
{ "L3V1 Spatial V1 Section"
}
},
Expand All @@ -894,7 +894,7 @@ static const packageErrorTableEntry spatialErrorTable[] =
"The 'unitSize' attributes should sum to 1.",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_WARNING,
"The values of the 'spatial:unitSize' attributes of every <compartmentMapping> with the same 'spatial:domainType' should sum to 1.",
"The values of the 'spatial:unitSize' attributes of every <compartmentMapping> with the same 'spatial:domainType' should sum to 1, when the dimensions of the referenced compartments are the same.",
{ "L3V1 Spatial V1 Section"
}
},
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24 changes: 24 additions & 0 deletions src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
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Expand Up @@ -664,6 +664,30 @@ END_CONSTRAINT
// 1221350
START_CONSTRAINT(SpatialCompartmentMappingUnitSizeMustBeFraction, CompartmentMapping, cmap)
{
SpatialModelPlugin *plug = (SpatialModelPlugin*)(m.getPlugin("spatial"));
pre(plug != NULL);
const Compartment *pComp = dynamic_cast<const Compartment*>(cmap.getParentSBMLObject());
pre(pComp != NULL);
pre(plug->isSetGeometry());
const Compartment* pOtherComp = NULL;
for (unsigned int i = 0; i < m.getNumCompartments(); ++i)
{
const Compartment* comp = m.getCompartment(i);
if (!comp) continue;
const SpatialCompartmentPlugin *compPlugin = dynamic_cast<const SpatialCompartmentPlugin *>(comp->getPlugin("spatial"));
if (!compPlugin) continue;
const CompartmentMapping* otherMapping = compPlugin->getCompartmentMapping();
if (!otherMapping) continue;
if (otherMapping->getDomainType() != cmap.getDomainType()) continue;
pOtherComp = comp;
break;
}
pre(pOtherComp != NULL);

// this constraint should only apply when
// the domainType's compartment has the same dimension as the mapped compartment
pre(pComp->getSpatialDimensions() == pOtherComp->getSpatialDimensions());

bool fail = false;
if (cmap.isSetUnitSize() && (cmap.getUnitSize() > 1 || cmap.getUnitSize() < 0)) {
fail = true;
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