Menu
▾
▴
[sbml-svn] SF.net SVN: sbml:[26135] branches/libsbml-experimental/src/sbml/packages/ spatial/validator
|
From: <luc...@us...> - 2019-10-22 22:14:39
|
Revision: 26135
http://sourceforge.net/p/sbml/code/26135
Author: luciansmith
Date: 2019-10-22 22:14:37 +0000 (Tue, 22 Oct 2019)
Log Message:
-----------
Spatial validation update:
* Consolidate 21752-21754
* Add 21350
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/test/test-data/general-constraints/1221350-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-02.xml
Removed Paths:
-------------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-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 2019-10-09 06:32:43 UTC (rev 26134)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-10-22 22:14:37 UTC (rev 26135)
@@ -121,6 +121,9 @@
, SpatialCompartmentMappingDomainTypeMustBeDomainType = 1221304
, SpatialCompartmentMappingUnitSizeMustBeDouble = 1221305
, SpatialCompartmentMappingNameMustBeString = 1221306
+, SpatialCompartmentMappingUnitSizeMustBeFraction = 1221350
+, SpatialCompartmentMappingUnitSizesSum = 1221351
+, SpatialCompartmentMappingUnitConsistency = 1221352
, SpatialCoordinateComponentAllowedCoreAttributes = 1221401
, SpatialCoordinateComponentAllowedCoreElements = 1221402
, SpatialCoordinateComponentAllowedAttributes = 1221403
@@ -160,9 +163,7 @@
, SpatialSampledVolumeMaxValueMustBeDouble = 1221708
, SpatialSampledVolumeNeedsMaxWithMin = 1221750
, SpatialSampledVolumeNeedsMinWithMax = 1221751
-, SpatialSampledVolumeNoSampledValueWithMinMax = 1221752
-, SpatialSampledVolumeNoMinMaxWithSampledValue = 1221753
-, SpatialSampledVolumeMinMaxOrSampledValue = 1221754
+, SpatialSampledVolumeSampledValueMinMax = 1221752
, SpatialAnalyticGeometryAllowedCoreAttributes = 1221801
, SpatialAnalyticGeometryAllowedCoreElements = 1221802
, SpatialAnalyticGeometryAllowedElements = 1221803
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-10-09 06:32:43 UTC (rev 26134)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-10-22 22:14:37 UTC (rev 26135)
@@ -753,6 +753,37 @@
}
},
+ // 1221350
+ { 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.",
+ { "L3V1 Spatial V1 Section"
+ }
+ },
+
+ // 1221351
+ { SpatialCompartmentMappingUnitSizesSum,
+ "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.",
+ { "L3V1 Spatial V1 Section"
+ }
+ },
+
+ // 1221352
+ { SpatialCompartmentMappingUnitConsistency,
+ "The units of a compartmentMapping should be compartment units over domain units.",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_WARNING,
+ "If a <parameter> has a child <spatialSymbolReference> that points to a <compartmentMapping>, the units of that <parameter> should be equivalent to the units of the parent <compartment> of the <compartmentMapping>, divided by the units of the <domainType> referenced by the <compartmentMapping>.",
+ { "L3V1 Spatial V1 Section"
+ }
+ },
+
// 1221401
{ SpatialCoordinateComponentAllowedCoreAttributes,
"Core attributes allowed on <coordinateComponent>.",
@@ -1218,35 +1249,15 @@
},
// 1221752
- { SpatialSampledVolumeNoSampledValueWithMinMax,
- "No 'sampledValue' attribute with min and max.",
+ { SpatialSampledVolumeSampledValueMinMax,
+ "Every <sampleVolume> must have a 'sampledValue' attribute or the 'min' and 'max' attributes.",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "A <sampledVolume> with defined 'spatial:minValue' and 'spatial:maxValue' attributes must not define the 'spatial:sampledValue' attribute.",
+ "A <sampledVolume> must either define the attribute 'spatial:sampledValue' or must define both the 'spatial:minValue' and 'spatial:maxValue' attributes, but may not define any other combination of those three attributes.",
{ "L3V1 Spatial V1 Section"
}
},
- // 1221753
- { SpatialSampledVolumeNoMinMaxWithSampledValue,
- "No 'minValue' nor 'maxValue' attributes with 'sampledValue'.",
- LIBSBML_CAT_GENERAL_CONSISTENCY,
- LIBSBML_SEV_ERROR,
- "A <sampledVolume> with a defined 'spatial:sampledValue' attribute may not define the 'spatial:minValue' nor the 'spatial:maxValue' attribute.",
- { "L3V1 Spatial V1 Section"
- }
- },
-
- // 1221754
- { SpatialSampledVolumeMinMaxOrSampledValue,
- "SampledVolume must have 'sampledVolume' or 'minValue' and 'maxValue'.",
- LIBSBML_CAT_GENERAL_CONSISTENCY,
- LIBSBML_SEV_ERROR,
- "A <sampledVolume> must either define its 'spatial:sampledValue' attribute or must define both the 'spatial:minValue' and 'spatial:maxValue' attributes.",
- { "L3V1 Spatial V1 Section"
- }
- },
-
// 1221801
{ SpatialAnalyticGeometryAllowedCoreAttributes,
"Core attributes allowed on <analyticGeometry>.",
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-10-09 06:32:43 UTC (rev 26134)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-10-22 22:14:37 UTC (rev 26135)
@@ -566,7 +566,7 @@
// 1221752
-START_CONSTRAINT(SpatialSampledVolumeNoSampledValueWithMinMax, SampledVolume, svol)
+START_CONSTRAINT(SpatialSampledVolumeSampledValueMinMax, SampledVolume, svol)
{
bool fail = false;
if (svol.isSetMaxValue() && svol.isSetMinValue() && svol.isSetSampledValue()) {
@@ -583,16 +583,7 @@
msg = ss_msg.str();
}
- inv(fail == false);
-}
-END_CONSTRAINT
-
-
-// 1221753
-START_CONSTRAINT(SpatialSampledVolumeNoMinMaxWithSampledValue, SampledVolume, svol)
-{
- bool fail = false;
- if (svol.isSetMaxValue() && !svol.isSetMinValue() && svol.isSetSampledValue()) {
+ else if (svol.isSetMaxValue() && !svol.isSetMinValue() && svol.isSetSampledValue()) {
fail = true;
stringstream ss_msg;
ss_msg << "A SampledVolume";
@@ -618,24 +609,36 @@
msg = ss_msg.str();
}
+ else if (!svol.isSetMaxValue() && !svol.isSetMinValue() && !svol.isSetSampledValue()) {
+ fail = true;
+ stringstream ss_msg;
+ ss_msg << "A SampledVolume";
+ if (svol.isSetId())
+ {
+ ss_msg << " with id '" << svol.getId() << "'";
+ }
+ ss_msg << " does not define a sampledValue, nor does it define a minValue and a maxValue.";
+ msg = ss_msg.str();
+ }
+
inv(fail == false);
}
END_CONSTRAINT
-// 1221754
-START_CONSTRAINT(SpatialSampledVolumeMinMaxOrSampledValue, SampledVolume, svol)
+// 1221350
+START_CONSTRAINT(SpatialCompartmentMappingUnitSizeMustBeFraction, CompartmentMapping, cmap)
{
bool fail = false;
- if (!svol.isSetMaxValue() && !svol.isSetMinValue() && !svol.isSetSampledValue()) {
+ if (cmap.isSetUnitSize() && (cmap.getUnitSize() > 1 || cmap.getUnitSize() < 0)) {
fail = true;
stringstream ss_msg;
- ss_msg << "A SampledVolume";
- if (svol.isSetId())
+ ss_msg << "A CompartmentMapping";
+ if (cmap.isSetId())
{
- ss_msg << " with id '" << svol.getId() << "'";
+ ss_msg << " with id '" << cmap.getId() << "'";
}
- ss_msg << " does not define a sampledValue, nor does it define a minValue and a maxValue.";
+ ss_msg << " has a unitSize of " << cmap.getUnitSize() << ".";
msg = ss_msg.str();
}
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-10-09 06:32:43 UTC (rev 26134)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-10-22 22:14:37 UTC (rev 26135)
@@ -54,9 +54,8 @@
addConstraint(new VConstraintSampledFieldSpatialSampledFieldThreeSamplesIn3DGeometry(*this));
addConstraint(new VConstraintSampledVolumeSpatialSampledVolumeNeedsMaxWithMin(*this));
addConstraint(new VConstraintSampledVolumeSpatialSampledVolumeNeedsMinWithMax(*this));
-addConstraint(new VConstraintSampledVolumeSpatialSampledVolumeNoSampledValueWithMinMax(*this));
-addConstraint(new VConstraintSampledVolumeSpatialSampledVolumeNoMinMaxWithSampledValue(*this));
-addConstraint(new VConstraintSampledVolumeSpatialSampledVolumeMinMaxOrSampledValue(*this));
+addConstraint(new VConstraintSampledVolumeSpatialSampledVolumeSampledValueMinMax(*this));
+addConstraint(new VConstraintCompartmentMappingSpatialCompartmentMappingUnitSizeMustBeFraction(*this));
/** @endcond */
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-fail-01-01.xml 2019-10-22 22:14:37 UTC (rev 26135)
@@ -0,0 +1,22 @@
+<?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:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="0"/>
+ </spatial:listOfDomainTypes>
+ </spatial:geometry>
+ <listOfCompartments>
+ <compartment constant="false" id="compartment">
+ <spatial:compartmentMapping spatial:domainType="domainType_1" spatial:id="compartmentMapping_1" spatial:unitSize="1.23"/>
+ </compartment>
+ </listOfCompartments>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-fail-01-02.xml 2019-10-22 22:14:37 UTC (rev 26135)
@@ -0,0 +1,22 @@
+<?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:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="0"/>
+ </spatial:listOfDomainTypes>
+ </spatial:geometry>
+ <listOfCompartments>
+ <compartment constant="false" id="compartment">
+ <spatial:compartmentMapping spatial:domainType="domainType_1" spatial:id="compartmentMapping_1" spatial:unitSize="-0.23"/>
+ </compartment>
+ </listOfCompartments>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-fail-01-03.xml 2019-10-22 22:14:37 UTC (rev 26135)
@@ -0,0 +1,22 @@
+<?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:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="0"/>
+ </spatial:listOfDomainTypes>
+ </spatial:geometry>
+ <listOfCompartments>
+ <compartment constant="false" id="compartment">
+ <spatial:compartmentMapping spatial:domainType="domainType_1" spatial:id="compartmentMapping_1" spatial:unitSize="23"/>
+ </compartment>
+ </listOfCompartments>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-fail-01-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-fail-01-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-fail-01-04.xml 2019-10-22 22:14:37 UTC (rev 26135)
@@ -0,0 +1,22 @@
+<?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:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="0"/>
+ </spatial:listOfDomainTypes>
+ </spatial:geometry>
+ <listOfCompartments>
+ <compartment constant="false" id="compartment">
+ <spatial:compartmentMapping spatial:domainType="domainType_1" spatial:id="compartmentMapping_1" spatial:unitSize="0.23e4"/>
+ </compartment>
+ </listOfCompartments>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-pass-00-01.xml 2019-10-22 22:14:37 UTC (rev 26135)
@@ -0,0 +1,22 @@
+<?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:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="0"/>
+ </spatial:listOfDomainTypes>
+ </spatial:geometry>
+ <listOfCompartments>
+ <compartment constant="false" id="compartment">
+ <spatial:compartmentMapping spatial:domainType="domainType_1" spatial:id="compartmentMapping_1" spatial:unitSize="0.23"/>
+ </compartment>
+ </listOfCompartments>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-pass-00-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221350-pass-00-02.xml 2019-10-22 22:14:37 UTC (rev 26135)
@@ -0,0 +1,22 @@
+<?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:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="0"/>
+ </spatial:listOfDomainTypes>
+ </spatial:geometry>
+ <listOfCompartments>
+ <compartment constant="false" id="compartment">
+ <spatial:compartmentMapping spatial:domainType="domainType_1" spatial:id="compartmentMapping_1" spatial:unitSize="2.3e-2"/>
+ </compartment>
+ </listOfCompartments>
+ </model>
+</sbml>
+
Copied: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-02.xml (from rev 26134, branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-01.xml)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-02.xml 2019-10-22 22:14:37 UTC (rev 26135)
@@ -0,0 +1,26 @@
+<?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:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <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:minValue="0" spatial:sampledValue="0"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Copied: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-03.xml (from rev 26134, branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-02.xml)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-03.xml 2019-10-22 22:14:37 UTC (rev 26135)
@@ -0,0 +1,26 @@
+<?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:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <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="0.5" spatial:sampledValue="0"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Copied: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-04.xml (from rev 26134, branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-01.xml)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-04.xml 2019-10-22 22:14:37 UTC (rev 26135)
@@ -0,0 +1,26 @@
+<?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:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <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:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Copied: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-02.xml (from rev 26134, branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-01.xml)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-02.xml 2019-10-22 22:14:37 UTC (rev 26135)
@@ -0,0 +1,26 @@
+<?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:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <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:sampledValue="0"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-01.xml 2019-10-09 06:32:43 UTC (rev 26134)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-01.xml 2019-10-22 22:14:37 UTC (rev 26135)
@@ -1,26 +0,0 @@
-<?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:listOfCoordinateComponents>
- <spatial:listOfDomainTypes>
- <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
- </spatial:listOfDomainTypes>
- <spatial:listOfGeometryDefinitions>
- <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:minValue="0" spatial:sampledValue="0"/>
- </spatial:listOfSampledVolumes>
- </spatial:sampledFieldGeometry>
- </spatial:listOfGeometryDefinitions>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
- </spatial:listOfSampledFields>
- </spatial:geometry>
- </model>
-</sbml>
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-02.xml 2019-10-09 06:32:43 UTC (rev 26134)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-02.xml 2019-10-22 22:14:37 UTC (rev 26135)
@@ -1,26 +0,0 @@
-<?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:listOfCoordinateComponents>
- <spatial:listOfDomainTypes>
- <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
- </spatial:listOfDomainTypes>
- <spatial:listOfGeometryDefinitions>
- <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="0.5" spatial:sampledValue="0"/>
- </spatial:listOfSampledVolumes>
- </spatial:sampledFieldGeometry>
- </spatial:listOfGeometryDefinitions>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
- </spatial:listOfSampledFields>
- </spatial:geometry>
- </model>
-</sbml>
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-01.xml 2019-10-09 06:32:43 UTC (rev 26134)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-01.xml 2019-10-22 22:14:37 UTC (rev 26135)
@@ -1,26 +0,0 @@
-<?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:listOfCoordinateComponents>
- <spatial:listOfDomainTypes>
- <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
- </spatial:listOfDomainTypes>
- <spatial:listOfGeometryDefinitions>
- <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:sampledValue="0"/>
- </spatial:listOfSampledVolumes>
- </spatial:sampledFieldGeometry>
- </spatial:listOfGeometryDefinitions>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
- </spatial:listOfSampledFields>
- </spatial:geometry>
- </model>
-</sbml>
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-01.xml 2019-10-09 06:32:43 UTC (rev 26134)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-01.xml 2019-10-22 22:14:37 UTC (rev 26135)
@@ -1,26 +0,0 @@
-<?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:listOfCoordinateComponents>
- <spatial:listOfDomainTypes>
- <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
- </spatial:listOfDomainTypes>
- <spatial:listOfGeometryDefinitions>
- <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:listOfSampledVolumes>
- </spatial:sampledFieldGeometry>
- </spatial:listOfGeometryDefinitions>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
- </spatial:listOfSampledFields>
- </spatial:geometry>
- </model>
-</sbml>
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-pass-00-01.xml 2019-10-09 06:32:43 UTC (rev 26134)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-pass-00-01.xml 2019-10-22 22:14:37 UTC (rev 26135)
@@ -1,26 +0,0 @@
-<?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:listOfCoordinateComponents>
- <spatial:listOfDomainTypes>
- <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
- </spatial:listOfDomainTypes>
- <spatial:listOfGeometryDefinitions>
- <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:sampledValue="0"/>
- </spatial:listOfSampledVolumes>
- </spatial:sampledFieldGeometry>
- </spatial:listOfGeometryDefinitions>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
- </spatial:listOfSampledFields>
- </spatial:geometry>
- </model>
-</sbml>
|
