Menu
▾
▴
[sbml-svn] SF.net SVN: sbml:[26142] branches/libsbml-experimental/src/sbml/packages/ spatial/validator
|
From: <luc...@us...> - 2019-10-24 18:57:09
|
Revision: 26142
http://sourceforge.net/p/sbml/code/26142
Author: luciansmith
Date: 2019-10-24 18:57:07 +0000 (Thu, 24 Oct 2019)
Log Message:
-----------
Add spatial validation rule 23350.
Modified Paths:
--------------
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/constraints/SpatialConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSpatialSymbolReferenceUniqueRefCheck.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSpatialSymbolReferenceUniqueRefCheck.h
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
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-10-24 17:25:24 UTC (rev 26141)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-10-24 18:57:07 UTC (rev 26142)
@@ -260,6 +260,7 @@
, SpatialSpatialSymbolReferenceAllowedCoreElements = 1223302
, SpatialSpatialSymbolReferenceAllowedAttributes = 1223303
, SpatialSpatialSymbolReferenceSpatialRefMustBeGeometry = 1223304
+, SpatialSpatialSymbolReferenceUniqueRef = 1223350
, SpatialDiffusionCoefficientAllowedCoreAttributes = 1223401
, SpatialDiffusionCoefficientAllowedCoreElements = 1223402
, SpatialDiffusionCoefficientAllowedAttributes = 1223403
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-10-24 17:25:24 UTC (rev 26141)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-10-24 18:57:07 UTC (rev 26142)
@@ -2410,6 +2410,16 @@
}
},
+ // 1223350
+ { SpatialSpatialSymbolReferenceUniqueRef,
+ "Every <spatialSymbolReference> must point to unique object.",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "Every <spatialSymbolReference> in a <model> must reference a unique spatial element.",
+ { "L3V1 Spatial V1 Section"
+ }
+ },
+
// 1223401
{ SpatialDiffusionCoefficientAllowedCoreAttributes,
"Core attributes allowed on <diffusionCoefficient>.",
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSpatialSymbolReferenceUniqueRefCheck.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSpatialSymbolReferenceUniqueRefCheck.cpp (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSpatialSymbolReferenceUniqueRefCheck.cpp 2019-10-24 18:57:07 UTC (rev 26142)
@@ -0,0 +1,107 @@
+/**
+* @cond doxygenLibsbmlInternal
+*
+* @file SpatialSpatialSymbolReferenceUniqueRefCheck.cpp
+* @brief Ensure that spatial compartment mappings' unit sizes sum to one.
+* @author Sarah Keating, Lucian Smith
+*
+* <!--------------------------------------------------------------------------
+* This file is part of libSBML. Please visit http://sbml.org for more
+* information about SBML, and the latest version of libSBML.
+*
+* Copyright (C) 2019 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. University of Heidelberg, Heidelberg, Germany
+*
+* Copyright (C) 2013-2018 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+* 3. University of Heidelberg, Heidelberg, Germany
+*
+* Copyright (C) 2009-2013 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+*
+* Copyright (C) 2006-2008 by the California Institute of Technology,
+* Pasadena, CA, USA
+*
+* Copyright (C) 2002-2005 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. Japan Science and Technology Agency, Japan
+*
+* This library is free software; you can redistribute it and/or modify it
+* under the terms of the GNU Lesser General Public License as published by
+* the Free Software Foundation. A copy of the license agreement is provided
+* in the file named "LICENSE.txt" included with this software distribution
+* and also available online as http://sbml.org/software/libsbml/license.html
+* ---------------------------------------------------------------------- -->*/
+
+#include "SpatialSpatialSymbolReferenceUniqueRefCheck.h"
+#include <sbml/packages/spatial/extension/SpatialParameterPlugin.h>
+
+#include <set>
+
+/** @cond doxygenIgnored */
+using namespace std;
+/** @endcond */
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+#ifdef __cplusplus
+
+
+/*
+* Creates a new Constraint with the given constraint id.
+*/
+SpatialSpatialSymbolReferenceUniqueRefCheck::SpatialSpatialSymbolReferenceUniqueRefCheck(unsigned int id, SpatialValidator & v):
+ TConstraint<Model>(id, v)
+{
+}
+
+/*
+* Destroys this Constraint.
+*/
+SpatialSpatialSymbolReferenceUniqueRefCheck::~SpatialSpatialSymbolReferenceUniqueRefCheck ()
+{
+}
+
+
+/*
+* Checks that all ids on the following Model objects are unique:
+* event assignments and assignment rules.
+*/
+void
+SpatialSpatialSymbolReferenceUniqueRefCheck::check_ (const Model& m, const Model&)
+{
+ if (m.getLevel() < 3) {
+ return;
+ }
+ set<string> referencedIDs;
+ set<string> duplicates;
+ for (unsigned long p = 0; p < m.getNumParameters(); p++) {
+ const Parameter* param = m.getParameter(p);
+ const SpatialParameterPlugin* spp = static_cast<const SpatialParameterPlugin*>(param->getPlugin("spatial"));
+ if (spp == NULL) {
+ continue;
+ }
+ if (spp->isSetSpatialSymbolReference()) {
+ const SpatialSymbolReference* ssr = spp->getSpatialSymbolReference();
+ if (ssr->isSetSpatialRef()) {
+ string ref = ssr->getSpatialRef();
+ if (referencedIDs.find(ref) != referencedIDs.end()) {
+ duplicates.insert(ref);
+ }
+ referencedIDs.insert(ref);
+ }
+ }
+ }
+ for (set<string>::iterator dup = duplicates.begin(); dup != duplicates.end(); dup++) {
+ msg = "Multiple <spatialSymbolReference> objects were found with the same spatialRef value, '";
+ msg += *dup + "'.";
+ logFailure(m);
+ }
+}
+
+#endif /* __cplusplus */
+
+LIBSBML_CPP_NAMESPACE_END
+/** @endcond */
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSpatialSymbolReferenceUniqueRefCheck.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSpatialSymbolReferenceUniqueRefCheck.h (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSpatialSymbolReferenceUniqueRefCheck.h 2019-10-24 18:57:07 UTC (rev 26142)
@@ -0,0 +1,69 @@
+/**
+* @cond doxygenLibsbmlInternal
+*
+* @file SpatialSpatialSymbolReferenceUniqueRefCheck.h
+* @brief Ensure that spatial compartment mappings' unit sizes sum to one.
+* @author Sarah Keating, Lucian Smith
+*
+* <!--------------------------------------------------------------------------
+* This file is part of libSBML. Please visit http://sbml.org for more
+* information about SBML, and the latest version of libSBML.
+*
+* Copyright (C) 2019 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. University of Heidelberg, Heidelberg, Germany
+*
+* Copyright (C) 2013-2018 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+* 3. University of Heidelberg, Heidelberg, Germany
+*
+* Copyright 2011-2012 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+*
+* This library is free software; you can redistribute it and/or modify it
+* under the terms of the GNU Lesser General Public License as published by
+* the Free Software Foundation. A copy of the license agreement is provided
+* in the file named "LICENSE.txt" included with this software distribution
+* and also available online as http://sbml.org/software/libsbml/license.html
+* ---------------------------------------------------------------------- -->*/
+
+#ifndef SpatialSpatialSymbolReferenceUniqueRefSum_h
+#define SpatialSpatialSymbolReferenceUniqueRefSum_h
+
+
+#ifdef __cplusplus
+
+#include <sbml/validator/VConstraint.h>
+#include <sbml/packages/spatial/validator/SpatialValidator.h>
+
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+
+class SpatialSpatialSymbolReferenceUniqueRefCheck: public TConstraint<Model>
+{
+public:
+
+ /**
+ * Creates a new Constraint with the given constraint id.
+ */
+ SpatialSpatialSymbolReferenceUniqueRefCheck (unsigned int id, SpatialValidator& v);
+
+ /**
+ * Destroys this Constraint.
+ */
+ virtual ~SpatialSpatialSymbolReferenceUniqueRefCheck ();
+
+
+protected:
+
+ virtual void check_ (const Model& m, const Model& object);
+
+};
+
+LIBSBML_CPP_NAMESPACE_END
+
+#endif /* __cplusplus */
+#endif /* SpatialSpatialSymbolReferenceUniqueRefSum_h */
+/** @endcond */
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 17:25:24 UTC (rev 26141)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-10-24 18:57:07 UTC (rev 26142)
@@ -45,6 +45,7 @@
#include <sbml/packages/spatial/common/SpatialExtensionTypes.h>
#include <sbml/packages/spatial/sbml/Geometry.h>
#include <sbml/packages/spatial/validator/SpatialCompartmentMappingUnitSizesCheck.h>
+#include <sbml/packages/spatial/validator/SpatialSpatialSymbolReferenceUniqueRefCheck.h>
#include <sbml/Species.h>
#endif /* AddingConstraintsToValidator */
@@ -54,6 +55,7 @@
using namespace std;
EXTERN_CONSTRAINT(ErrorEnumValue, SpatialCompartmentMappingUnitSizesCheck);
+EXTERN_CONSTRAINT(ErrorEnumValue, SpatialSpatialSymbolReferenceUniqueRefCheck);
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 17:25:24 UTC (rev 26141)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-10-24 18:57:07 UTC (rev 26142)
@@ -39,6 +39,7 @@
*/
#include "sbml\packages\spatial\validator\SpatialCompartmentMappingUnitSizesCheck.h"
+#include "sbml\packages\spatial\validator\SpatialSpatialSymbolReferenceUniqueRefCheck.h"
addConstraint(new VConstraintDomainSpatialDomainDomainTypeMustBeDomainType(*this));
addConstraint(new VConstraintAdjacentDomainsSpatialAdjacentDomainsDomain1MustBeDomain(*this));
@@ -61,6 +62,7 @@
addConstraint(new VConstraintSpeciesSpatialCompartmentsMustHaveCompartmentMapping(*this));
addConstraint(new SpatialCompartmentMappingUnitSizesCheck(1221351, *this));
+addConstraint(new SpatialSpatialSymbolReferenceUniqueRefCheck(SpatialSpatialSymbolReferenceUniqueRef, *this));
/** @endcond */
Added: 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-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223350-fail-01-01.xml 2019-10-24 18:57:07 UTC (rev 26142)
@@ -0,0 +1,79 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <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: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:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfAdjacentDomains>
+ <spatial:adjacentDomains spatial:domain1="domain_1" spatial:domain2="domain_1" spatial:id="adjacentDomains_1"/>
+ </spatial:listOfAdjacentDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="false">
+ <spatial:listOfAnalyticVolumes>
+ <spatial:analyticVolume spatial:domainType="domainType_1" spatial:functionType="layered" spatial:id="analyticVolume_1" spatial:ordinal="0">
+ <math xmlns="http://www.w3.org/1998/Math/MathML"/>
+ </spatial:analyticVolume>
+ </spatial:listOfAnalyticVolumes>
+ </spatial:analyticGeometry>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:maxValue="0" spatial:minValue="0"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ <spatial:parametricGeometry spatial:id="geometryDefinition_3" spatial:isActive="false">
+ <spatial:spatialPoints spatial:arrayDataLength="0" spatial:compression="uncompressed" spatial:dataType="double" spatial:id="spatialPoints_1"/>
+ <spatial:listOfParametricObjects>
+ <spatial:parametricObject spatial:compression="uncompressed" spatial:dataType="double" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:pointIndexLength="0" spatial:polygonType="triangle"/>
+ </spatial:listOfParametricObjects>
+ </spatial:parametricGeometry>
+ <spatial:mixedGeometry spatial:id="geometryDefinition_4" spatial:isActive="false">
+ <spatial:listOfOrdinalMappings>
+ <spatial:ordinalMapping spatial:geometryDefinition="geometryDefinition_4" spatial:ordinal="0"/>
+ </spatial:listOfOrdinalMappings>
+ </spatial:mixedGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="0" spatial:numSamples2="0" spatial:numSamples3="0" spatial:samplesLength="3"/>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ <listOfCompartments>
+ <compartment constant="false" id="compartment">
+ <spatial:compartmentMapping spatial:domainType="domainType_1" spatial:id="compartmentMapping_1" spatial:unitSize="1"/>
+ </compartment>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="id_3">
+ <spatial:spatialSymbolReference spatial:spatialRef="coordinateComponent_1"/>
+ </parameter>
+ <parameter constant="false" id="id_4">
+ <spatial:spatialSymbolReference spatial:spatialRef="coordinateComponent_1"/>
+ </parameter>
+ </listOfParameters>
+ </model>
+</sbml>
+
Added: 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-fail-02-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223350-fail-02-02.xml 2019-10-24 18:57:07 UTC (rev 26142)
@@ -0,0 +1,85 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <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: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:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfAdjacentDomains>
+ <spatial:adjacentDomains spatial:domain1="domain_1" spatial:domain2="domain_1" spatial:id="adjacentDomains_1"/>
+ </spatial:listOfAdjacentDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="false">
+ <spatial:listOfAnalyticVolumes>
+ <spatial:analyticVolume spatial:domainType="domainType_1" spatial:functionType="layered" spatial:id="analyticVolume_1" spatial:ordinal="0">
+ <math xmlns="http://www.w3.org/1998/Math/MathML"/>
+ </spatial:analyticVolume>
+ </spatial:listOfAnalyticVolumes>
+ </spatial:analyticGeometry>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:maxValue="0" spatial:minValue="0"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ <spatial:parametricGeometry spatial:id="geometryDefinition_3" spatial:isActive="false">
+ <spatial:spatialPoints spatial:arrayDataLength="0" spatial:compression="uncompressed" spatial:dataType="double" spatial:id="spatialPoints_1"/>
+ <spatial:listOfParametricObjects>
+ <spatial:parametricObject spatial:compression="uncompressed" spatial:dataType="double" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:pointIndexLength="0" spatial:polygonType="triangle"/>
+ </spatial:listOfParametricObjects>
+ </spatial:parametricGeometry>
+ <spatial:mixedGeometry spatial:id="geometryDefinition_4" spatial:isActive="false">
+ <spatial:listOfOrdinalMappings>
+ <spatial:ordinalMapping spatial:geometryDefinition="geometryDefinition_4" spatial:ordinal="0"/>
+ </spatial:listOfOrdinalMappings>
+ </spatial:mixedGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="0" spatial:numSamples2="0" spatial:numSamples3="0" spatial:samplesLength="3"/>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ <listOfCompartments>
+ <compartment constant="false" id="compartment">
+ <spatial:compartmentMapping spatial:domainType="domainType_1" spatial:id="compartmentMapping_1" spatial:unitSize="1"/>
+ </compartment>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="id_3">
+ <spatial:spatialSymbolReference spatial:spatialRef="coordinateComponent_1"/>
+ </parameter>
+ <parameter constant="false" id="id_4">
+ <spatial:spatialSymbolReference spatial:spatialRef="coordinateComponent_1"/>
+ </parameter>
+ <parameter constant="false" id="id_5">
+ <spatial:spatialSymbolReference spatial:spatialRef="geometry_1"/>
+ </parameter>
+ <parameter constant="false" id="id_6">
+ <spatial:spatialSymbolReference spatial:spatialRef="geometry_1"/>
+ </parameter>
+ </listOfParameters>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223350-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223350-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223350-pass-00-01.xml 2019-10-24 18:57:07 UTC (rev 26142)
@@ -0,0 +1,79 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <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: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:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfAdjacentDomains>
+ <spatial:adjacentDomains spatial:domain1="domain_1" spatial:domain2="domain_1" spatial:id="adjacentDomains_1"/>
+ </spatial:listOfAdjacentDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="false">
+ <spatial:listOfAnalyticVolumes>
+ <spatial:analyticVolume spatial:domainType="domainType_1" spatial:functionType="layered" spatial:id="analyticVolume_1" spatial:ordinal="0">
+ <math xmlns="http://www.w3.org/1998/Math/MathML"/>
+ </spatial:analyticVolume>
+ </spatial:listOfAnalyticVolumes>
+ </spatial:analyticGeometry>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:maxValue="0" spatial:minValue="0"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ <spatial:parametricGeometry spatial:id="geometryDefinition_3" spatial:isActive="false">
+ <spatial:spatialPoints spatial:arrayDataLength="0" spatial:compression="uncompressed" spatial:dataType="double" spatial:id="spatialPoints_1"/>
+ <spatial:listOfParametricObjects>
+ <spatial:parametricObject spatial:compression="uncompressed" spatial:dataType="double" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:pointIndexLength="0" spatial:polygonType="triangle"/>
+ </spatial:listOfParametricObjects>
+ </spatial:parametricGeometry>
+ <spatial:mixedGeometry spatial:id="geometryDefinition_4" spatial:isActive="false">
+ <spatial:listOfOrdinalMappings>
+ <spatial:ordinalMapping spatial:geometryDefinition="geometryDefinition_4" spatial:ordinal="0"/>
+ </spatial:listOfOrdinalMappings>
+ </spatial:mixedGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="0" spatial:numSamples2="0" spatial:numSamples3="0" spatial:samplesLength="3"/>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ <listOfCompartments>
+ <compartment constant="false" id="compartment">
+ <spatial:compartmentMapping spatial:domainType="domainType_1" spatial:id="compartmentMapping_1" spatial:unitSize="1"/>
+ </compartment>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="id_3">
+ <spatial:spatialSymbolReference spatial:spatialRef="geometry_1"/>
+ </parameter>
+ <parameter constant="false" id="id_4">
+ <spatial:spatialSymbolReference spatial:spatialRef="coordinateComponent_1"/>
+ </parameter>
+ </listOfParameters>
+ </model>
+</sbml>
+
|
