Merge pull request #276 from sbmlteam/spatial-validation-issue

#275: check that spatial dimensions match before running test
sbmlteam · Oct 28, 2022 · efc1992 · efc1992
2 parents 6135015 + 4733698
commit efc1992
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Showing 2 changed files with 28 additions and 4 deletions.
diff --git a/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h b/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
@@ -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"
     }
   },
@@ -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"
     }
   },

diff --git a/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp b/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
@@ -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;