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[sbml-svn] SF.net SVN: sbml:[26143] branches/libsbml-experimental/src/sbml/packages/ spatial
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From: <luc...@us...> - 2019-10-24 20:39:28
|
Revision: 26143
http://sourceforge.net/p/sbml/code/26143
Author: luciansmith
Date: 2019-10-24 20:39:24 +0000 (Thu, 24 Oct 2019)
Log Message:
-----------
Add modified spatial validation rule 23304. Also fix a lot of old files so they don't fail the new rule. Also also, actually call validation for spatial parameters.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SpatialSymbolReference.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialValidator.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220301-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220301-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220450-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220450-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-05.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-06.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-07.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-08.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-09.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-10.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-pass-00-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220801-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220801-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220801-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220801-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220802-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220802-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220802-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220803-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220803-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220803-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220803-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220804-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220804-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220805-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220805-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220806-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220806-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220806-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220807-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220807-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220808-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220808-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220808-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220808-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220901-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220901-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220901-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220901-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220902-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220902-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220902-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220903-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220903-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220903-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220903-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220903-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220904-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220904-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220905-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220905-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220906-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220906-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221101-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221101-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221101-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221101-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221102-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221102-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221102-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221103-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221103-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221103-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221103-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221103-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221104-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221104-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221105-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221105-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221201-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221201-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221201-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221201-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221202-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221202-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221202-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221203-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221203-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221203-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221203-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221204-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221204-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223350-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223350-fail-02-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223350-pass-00-01.xml
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-pass-00-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-pass-00-05.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-pass-00-06.xml
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SpatialSymbolReference.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SpatialSymbolReference.cpp 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SpatialSymbolReference.cpp 2019-10-24 20:39:24 UTC (rev 26143)
@@ -638,7 +638,7 @@
msg += " is '" + mSpatialRef + "', which does not conform to the "
"syntax.";
log->logPackageError("spatial",
- SpatialSpatialSymbolReferenceSpatialRefMustBeGeometry, pkgVersion, level,
+ SpatialSpatialSymbolReferenceSpatialRefMustReferenceMath, pkgVersion, level,
version, msg, getLine(), getColumn());
}
}
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-10-24 20:39:24 UTC (rev 26143)
@@ -259,7 +259,7 @@
, SpatialSpatialSymbolReferenceAllowedCoreAttributes = 1223301
, SpatialSpatialSymbolReferenceAllowedCoreElements = 1223302
, SpatialSpatialSymbolReferenceAllowedAttributes = 1223303
-, SpatialSpatialSymbolReferenceSpatialRefMustBeGeometry = 1223304
+, SpatialSpatialSymbolReferenceSpatialRefMustReferenceMath = 1223304
, SpatialSpatialSymbolReferenceUniqueRef = 1223350
, SpatialDiffusionCoefficientAllowedCoreAttributes = 1223401
, SpatialDiffusionCoefficientAllowedCoreElements = 1223402
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-10-24 20:39:24 UTC (rev 26143)
@@ -2399,13 +2399,13 @@
},
// 1223304
- { SpatialSpatialSymbolReferenceSpatialRefMustBeGeometry,
- "The attribute 'spatialRef' must point to Geometry object.",
+ { SpatialSpatialSymbolReferenceSpatialRefMustReferenceMath,
+ "The attribute 'spatialRef' must point to a spatial object with mathematical meaning.",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
"The value of the attribute 'spatial:spatialRef' of a "
"<spatialSymbolReference> object must be the identifier of an existing "
- "<geometry> object defined in the enclosing <model> object.",
+ "<compartmentMapping>, <coordinateComponent>, <boundary>, <domainType>, <domain>, or <sampledField> object defined in the enclosing <model> object.",
{ "L3V1 Spatial V1 Section"
}
},
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialValidator.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialValidator.cpp 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialValidator.cpp 2019-10-24 20:39:24 UTC (rev 26143)
@@ -1018,6 +1018,16 @@
m->getReaction(i)->accept(vv);
}
}
+
+ for (i = 0; i < m->getNumParameters(); i++)
+ {
+ const SpatialParameterPlugin* spPlug = static_cast<const
+ SpatialParameterPlugin*>(m->getParameter(i)->getPlugin("spatial"));
+ if (spPlug != NULL)
+ {
+ spPlug->accept(vv);
+ }
+ }
}
return (unsigned int)(mFailures.size());
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-10-24 20:39:24 UTC (rev 26143)
@@ -659,24 +659,20 @@
START_CONSTRAINT(SpatialCompartmentsMustHaveCompartmentMapping, Species, species)
{
bool fail = false;
- if (!species.isSetCompartment()) {
- return;
- }
+ pre(species.isSetCompartment());
+
const SpatialSpeciesPlugin* ssp = static_cast<const SpatialSpeciesPlugin*>(species.getPlugin("spatial"));
- if (ssp == NULL || !ssp->isSetIsSpatial() || !ssp->getIsSpatial()) {
- return;
- }
- if (species.getParentSBMLObject() == NULL) {
- return;
- }
+ pre(ssp != NULL);
+ pre(ssp->isSetIsSpatial());
+ pre(ssp->getIsSpatial());
+ pre(species.getParentSBMLObject() != NULL);
+
const Model* model = static_cast<const Model*>(species.getParentSBMLObject()->getParentSBMLObject());
- if (model == NULL) {
- return;
- }
+ pre(model != NULL);
+
const Compartment* compartment = model->getCompartment(species.getCompartment());
- if (compartment == NULL) {
- return;
- }
+ pre(compartment != NULL);
+
const SpatialCompartmentPlugin* scp = static_cast<const SpatialCompartmentPlugin*>(compartment->getPlugin("spatial"));
if (scp == NULL || scp->isSetCompartmentMapping() == false) {
fail = true;
@@ -694,6 +690,50 @@
}
END_CONSTRAINT
+// 1223304
+START_CONSTRAINT(SpatialSpatialSymbolReferenceSpatialRefMustReferenceMath, SpatialSymbolReference, ssr)
+{
+ pre(ssr.isSetSpatialRef());
+ msg = "A <spatialSymbolReference>";
+ if (ssr.isSetId()) {
+ msg += " with the id '" + ssr.getId() + "'";
+ }
+ msg += " has a 'spatialRef' value of '" + ssr.getSpatialRef() + "'";
+ bool fail = false;
+ const SBase* parent = ssr.getParentSBMLObject(); //The Parameter
+ pre(parent != NULL);
+ parent = parent->getParentSBMLObject(); //The ListOfParameters
+ pre(parent != NULL);
+ parent = parent->getParentSBMLObject(); //The Model
+ pre(parent != NULL);
+ SBase* ncparent = const_cast<SBase*>(parent); //Need non-const version for 'getElementBySId'.
+ Model* model = static_cast<Model*>(ncparent);
+ pre(model != NULL);
+ const SBase* ref = model->getElementBySId(ssr.getSpatialRef());
+ if (ref == NULL) {
+ fail = true;
+ msg += ", but no object with that ID could be found.";
+ }
+ else {
+ switch (ref->getTypeCode()) {
+ case SBML_SPATIAL_COMPARTMENTMAPPING:
+ case SBML_SPATIAL_COORDINATECOMPONENT:
+ case SBML_SPATIAL_BOUNDARY:
+ case SBML_SPATIAL_DOMAINTYPE:
+ case SBML_SPATIAL_DOMAIN:
+ case SBML_SPATIAL_SAMPLEDFIELD:
+ return;
+ }
+ fail = true;
+ msg += ", which is not a spatial element with mathematical meaning.";
+ }
+
+ inv(fail == false);
+}
+END_CONSTRAINT
+
+
+
/** @endcond */
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-10-24 20:39:24 UTC (rev 26143)
@@ -60,7 +60,9 @@
addConstraint(new VConstraintSampledVolumeSpatialSampledVolumeSampledValueMinMax(*this));
addConstraint(new VConstraintCompartmentMappingSpatialCompartmentMappingUnitSizeMustBeFraction(*this));
addConstraint(new VConstraintSpeciesSpatialCompartmentsMustHaveCompartmentMapping(*this));
+addConstraint(new VConstraintSpatialSymbolReferenceSpatialSpatialSymbolReferenceSpatialRefMustReferenceMath(*this));
+
addConstraint(new SpatialCompartmentMappingUnitSizesCheck(1221351, *this));
addConstraint(new SpatialSpatialSymbolReferenceUniqueRefCheck(SpatialSpatialSymbolReferenceUniqueRef, *this));
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220301-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220301-fail-01-01.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220301-fail-01-01.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220301-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220301-pass-00-01.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220301-pass-00-01.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220450-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220450-fail-01-01.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220450-fail-01-01.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220450-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220450-pass-00-01.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220450-pass-00-01.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-01.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-01.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
@@ -68,8 +68,8 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:spatialSymbolReference spatial:spatialRef="geometry_1"/>
- <spatial:spatialSymbolReference spatial:spatialRef="geometry_1"/>
+ <spatial:spatialSymbolReference spatial:spatialRef="coordinateComponent_2"/>
+ <spatial:spatialSymbolReference spatial:spatialRef="coordinateComponent_2"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-02.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-02.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-03.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-03.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-04.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-04.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-05.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-05.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-05.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
@@ -68,7 +68,7 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:spatialSymbolReference spatial:spatialRef="geometry_1"/>
+ <spatial:spatialSymbolReference spatial:spatialRef="coordinateComponent_2"/>
<spatial:advectionCoefficient spatial:coordinate="cartesianX" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-06.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-06.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-06.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
@@ -68,7 +68,7 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:spatialSymbolReference spatial:spatialRef="geometry_1"/>
+ <spatial:spatialSymbolReference spatial:spatialRef="coordinateComponent_2"/>
<spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Robin_valueCoefficient" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-07.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-07.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-07.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
@@ -68,7 +68,7 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:spatialSymbolReference spatial:spatialRef="geometry_1"/>
+ <spatial:spatialSymbolReference spatial:spatialRef="coordinateComponent_2"/>
<spatial:diffusionCoefficient spatial:coordinateReference1="cartesianX" spatial:coordinateReference2="cartesianX" spatial:type="isotropic" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-08.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-08.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-08.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-09.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-09.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-09.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-10.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-10.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-10.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-pass-00-01.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-pass-00-01.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
@@ -68,7 +68,7 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:spatialSymbolReference spatial:spatialRef="geometry_1"/>
+ <spatial:spatialSymbolReference spatial:spatialRef="coordinateComponent_2"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-pass-00-02.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-pass-00-02.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-pass-00-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-pass-00-03.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-pass-00-03.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-pass-00-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-pass-00-04.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-pass-00-04.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220801-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220801-fail-01-01.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220801-fail-01-01.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220801-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220801-pass-00-01.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220801-pass-00-01.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
<spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220801-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220801-pass-00-02.xml 2019-10-24 18:57:07 UTC (rev 26142)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220801-pass-00-02.xml 2019-10-24 20:39:24 UTC (rev 26143)
@@ -7,11 +7,11 @@
<spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
</spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensi...
[truncated message content] |
