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|
From: <luc...@us...> - 2020-01-27 19:17:47
|
Revision: 26272
http://sourceforge.net/p/sbml/code/26272
Author: luciansmith
Date: 2020-01-27 19:17:45 +0000 (Mon, 27 Jan 2020)
Log Message:
-----------
Fix warning.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ParametricObject.cpp
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ParametricObject.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ParametricObject.cpp 2020-01-27 19:15:55 UTC (rev 26271)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ParametricObject.cpp 2020-01-27 19:17:45 UTC (rev 26272)
@@ -824,7 +824,7 @@
if (isSetPointIndex())
{
- for (int i = 0; i < mNumPointIndexEntries; ++i)
+ for (size_t i = 0; i < mNumPointIndexEntries; ++i)
{
stream << (long)mPointIndex[i] << " ";
}
|
|
From: <luc...@us...> - 2020-01-27 19:15:57
|
Revision: 26271
http://sourceforge.net/p/sbml/code/26271
Author: luciansmith
Date: 2020-01-27 19:15:55 +0000 (Mon, 27 Jan 2020)
Log Message:
-----------
Add heading for some compilers.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ParametricObject.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ParametricObject.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ParametricObject.cpp 2020-01-27 17:25:06 UTC (rev 26270)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ParametricObject.cpp 2020-01-27 19:15:55 UTC (rev 26271)
@@ -37,6 +37,7 @@
#include <sbml/packages/spatial/sbml/ParametricObject.h>
#include <sbml/packages/spatial/sbml/ListOfParametricObjects.h>
#include <sbml/packages/spatial/validator/SpatialSBMLError.h>
+#include <math.h>
using namespace std;
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2020-01-27 17:25:06 UTC (rev 26270)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2020-01-27 19:15:55 UTC (rev 26271)
@@ -39,6 +39,7 @@
*/
#ifndef AddingConstraintsToValidator
#include <set>
+#include <math.h>
#include <sbml/validator/VConstraint.h>
|
|
From: <luc...@us...> - 2020-01-27 17:25:08
|
Revision: 26270
http://sourceforge.net/p/sbml/code/26270
Author: luciansmith
Date: 2020-01-27 17:25:06 +0000 (Mon, 27 Jan 2020)
Log Message:
-----------
Give these 'fail' files the correct name.
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-05.xml
Removed Paths:
-------------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-05.xml
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-01.xml 2020-01-17 22:32:42 UTC (rev 26269)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-01.xml 2020-01-27 17:25:06 UTC (rev 26270)
@@ -1,22 +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: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_3" spatial:type="cartesianY" 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:geometry>
- </model>
-</sbml>
-
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-02.xml 2020-01-17 22:32:42 UTC (rev 26269)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-02.xml 2020-01-27 17:25:06 UTC (rev 26270)
@@ -1,22 +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: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_3" spatial:type="cartesianX" 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:geometry>
- </model>
-</sbml>
-
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-03.xml 2020-01-17 22:32:42 UTC (rev 26269)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-03.xml 2020-01-27 17:25:06 UTC (rev 26270)
@@ -1,22 +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:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianZ" 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_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>
- </spatial:listOfCoordinateComponents>
- </spatial:geometry>
- </model>
-</sbml>
-
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-04.xml 2020-01-17 22:32:42 UTC (rev 26269)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-04.xml 2020-01-27 17:25:06 UTC (rev 26270)
@@ -1,22 +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:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianX" 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_3" spatial:type="cartesianX" 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:geometry>
- </model>
-</sbml>
-
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-05.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-05.xml 2020-01-17 22:32:42 UTC (rev 26269)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-05.xml 2020-01-27 17:25:06 UTC (rev 26270)
@@ -1,22 +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="cartesianZ" 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_2" spatial:type="cartesianZ" 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_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>
- </spatial:listOfCoordinateComponents>
- </spatial:geometry>
- </model>
-</sbml>
-
Copied: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-01.xml (from rev 26269, branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-01.xml)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-01.xml 2020-01-27 17:25:06 UTC (rev 26270)
@@ -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: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_3" spatial:type="cartesianY" 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:geometry>
+ </model>
+</sbml>
+
Copied: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-02.xml (from rev 26269, branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-02.xml)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-02.xml 2020-01-27 17:25:06 UTC (rev 26270)
@@ -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: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_3" spatial:type="cartesianX" 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:geometry>
+ </model>
+</sbml>
+
Copied: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-03.xml (from rev 26269, branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-03.xml)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-03.xml 2020-01-27 17:25:06 UTC (rev 26270)
@@ -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:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianZ" 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_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>
+ </spatial:listOfCoordinateComponents>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Copied: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-04.xml (from rev 26269, branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-04.xml)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-04.xml 2020-01-27 17:25:06 UTC (rev 26270)
@@ -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:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianX" 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_3" spatial:type="cartesianX" 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:geometry>
+ </model>
+</sbml>
+
Copied: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-05.xml (from rev 26269, branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-05.xml)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-05.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-01-05.xml 2020-01-27 17:25:06 UTC (rev 26270)
@@ -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="cartesianZ" 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_2" spatial:type="cartesianZ" 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_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>
+ </spatial:listOfCoordinateComponents>
+ </spatial:geometry>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2020-01-17 22:32:44
|
Revision: 26269
http://sourceforge.net/p/sbml/code/26269
Author: luciansmith
Date: 2020-01-17 22:32:42 +0000 (Fri, 17 Jan 2020)
Log Message:
-----------
Better python text output.
Modified Paths:
--------------
branches/libsbml-experimental-lucian/src/sbml/math/L3FormulaFormatter.cpp
Modified: branches/libsbml-experimental-lucian/src/sbml/math/L3FormulaFormatter.cpp
===================================================================
--- branches/libsbml-experimental-lucian/src/sbml/math/L3FormulaFormatter.cpp 2020-01-16 21:03:29 UTC (rev 26268)
+++ branches/libsbml-experimental-lucian/src/sbml/math/L3FormulaFormatter.cpp 2020-01-17 22:32:42 UTC (rev 26269)
@@ -549,6 +549,37 @@
break;
}
}
+ if (settings != NULL && settings->getPythonFormat() != PythonFormatSBML) {
+ switch (type) {
+ case AST_FUNCTION_ARCCOSH:
+ StringBuffer_append(sb, "acosh");
+ return;
+ case AST_FUNCTION_ARCCOT:
+ StringBuffer_append(sb, "acot");
+ return;
+ case AST_FUNCTION_ARCCOTH:
+ StringBuffer_append(sb, "acoth");
+ return;
+ case AST_FUNCTION_ARCCSC:
+ StringBuffer_append(sb, "acsc");
+ return;
+ case AST_FUNCTION_ARCCSCH:
+ StringBuffer_append(sb, "acsch");
+ return;
+ case AST_FUNCTION_ARCSEC:
+ StringBuffer_append(sb, "asec");
+ return;
+ case AST_FUNCTION_ARCSECH:
+ StringBuffer_append(sb, "asech");
+ return;
+ case AST_FUNCTION_ARCSINH:
+ StringBuffer_append(sb, "asinh");
+ return;
+ case AST_FUNCTION_ARCTANH:
+ StringBuffer_append(sb, "atanh");
+ return;
+ }
+ }
switch (type)
{
case AST_PLUS:
|
|
From: <luc...@us...> - 2020-01-16 21:03:32
|
Revision: 26268
http://sourceforge.net/p/sbml/code/26268
Author: luciansmith
Date: 2020-01-16 21:03:29 +0000 (Thu, 16 Jan 2020)
Log Message:
-----------
* Add generic 'apply' function for when the function doesn't have a name, but instead it's found via some lookup, i.e. "foo[bar](3)".
* Add different 'EQ' class so that we can output either "x == y" or "x = y" as needed.
* Add Python output for selectors (x[y])
* Add ability to store boolean eq's in sets without them being mistaken for dictionary entries (via classes, again).
Modified Paths:
--------------
branches/libsbml-experimental-lucian/src/sbml/math/ASTNodeType.h
branches/libsbml-experimental-lucian/src/sbml/math/L3FormulaFormatter.cpp
branches/libsbml-experimental-lucian/src/sbml/math/L3FormulaFormatter.h
branches/libsbml-experimental-lucian/src/sbml/math/test/TestL3PythonFormulaFormatter.cpp
branches/libsbml-experimental-lucian/src/sbml/packages/l3v2extendedmath/extension/L3v2extendedmathASTPlugin.cpp
Modified: branches/libsbml-experimental-lucian/src/sbml/math/ASTNodeType.h
===================================================================
--- branches/libsbml-experimental-lucian/src/sbml/math/ASTNodeType.h 2020-01-09 15:03:00 UTC (rev 26267)
+++ branches/libsbml-experimental-lucian/src/sbml/math/ASTNodeType.h 2020-01-16 21:03:29 UTC (rev 26268)
@@ -158,6 +158,7 @@
/* generic to facilitate non sbml libraries*/
, AST_CSYMBOL_FUNCTION = 400
+ , AST_APPLY_FUNCTION
/* Distrib */
, AST_DISTRIB_FUNCTION_NORMAL = 500
Modified: branches/libsbml-experimental-lucian/src/sbml/math/L3FormulaFormatter.cpp
===================================================================
--- branches/libsbml-experimental-lucian/src/sbml/math/L3FormulaFormatter.cpp 2020-01-09 15:03:00 UTC (rev 26267)
+++ branches/libsbml-experimental-lucian/src/sbml/math/L3FormulaFormatter.cpp 2020-01-16 21:03:29 UTC (rev 26268)
@@ -747,7 +747,12 @@
}
break;
case AST_RELATIONAL_EQ:
- StringBuffer_append(sb, "==");
+ if (node->getClass() == "assignment") {
+ StringBuffer_append(sb, "=");
+ }
+ else {
+ StringBuffer_append(sb, "==");
+ }
break;
case AST_RELATIONAL_GEQ:
StringBuffer_append(sb, ">=");
@@ -791,7 +796,10 @@
{
ASTNodeType_t type = ASTNode_getType(node);
- if (ASTNode_isLog10(node))
+ if (type == AST_APPLY_FUNCTION) {
+ L3FormulaFormatter_visitGenericApply(parent, node, sb, settings);
+ }
+ else if (ASTNode_isLog10(node))
{
L3FormulaFormatter_visitLog10(parent, node, sb, settings);
}
@@ -811,6 +819,10 @@
{
L3FormulaFormatter_visitPythonVector(parent, node, sb, settings);
}
+ else if (settings != NULL && settings->getPythonFormat() != PythonFormatSBML && type == AST_LINEAR_ALGEBRA_SELECTOR)
+ {
+ L3FormulaFormatter_visitPythonSelector(parent, node, sb, settings);
+ }
else if (settings != NULL && settings->getPythonFormat() != PythonFormatSBML && type == AST_SET_THEORY_SET)
{
L3FormulaFormatter_visitPythonSet(parent, node, sb, settings);
@@ -901,6 +913,27 @@
* formats it as "log10(x)" (where x is any subexpression).
*/
void
+L3FormulaFormatter_visitGenericApply( const ASTNode_t *parent,
+ const ASTNode_t *node,
+ StringBuffer_t *sb,
+ const L3ParserSettings_t *settings )
+{
+ L3FormulaFormatter_visit(node, node->getChild(0), sb, settings);
+ StringBuffer_append(sb, "(");
+ for (unsigned long c = 1; c < node->getNumChildren(); c++) {
+ if (c > 1) {
+ StringBuffer_append(sb, ", ");
+ }
+ L3FormulaFormatter_visit(node, node->getChild(c), sb, settings);
+ }
+ StringBuffer_appendChar(sb, ')');
+}
+
+/**
+* Visits the given ASTNode as the function "log(10, x)" and in doing so,
+* formats it as "log10(x)" (where x is any subexpression).
+*/
+void
L3FormulaFormatter_visitLog10 ( const ASTNode_t *parent,
const ASTNode_t *node,
StringBuffer_t *sb,
@@ -941,6 +974,33 @@
}
+void L3FormulaFormatter_visitPythonSelector(const ASTNode_t * parent, const ASTNode_t * node, StringBuffer_t * sb, const L3ParserSettings_t * settings)
+{
+ if (node->getNumChildren() > 0) {
+ L3FormulaFormatter_visit(node, node->getChild(0), sb, settings);
+ }
+ if (node->isSetClass() && node->getClass() == "byDot") {
+ StringBuffer_appendChar(sb, '.');
+ for (unsigned int c = 1; c < node->getNumChildren(); c++) {
+ if (c > 1) {
+ StringBuffer_appendChar(sb, '.');
+ }
+ L3FormulaFormatter_visit(node, node->getChild(c), sb, settings);
+ }
+ }
+ else {
+ StringBuffer_appendChar(sb, '[');
+ for (unsigned int c = 1; c < node->getNumChildren(); c++) {
+ if (c > 1) {
+ StringBuffer_append(sb, ", ");
+ }
+ L3FormulaFormatter_visit(node, node->getChild(c), sb, settings);
+ }
+ StringBuffer_appendChar(sb, ']');
+ }
+}
+
+
void L3FormulaFormatter_visitPythonSet(const ASTNode_t * parent, const ASTNode_t * node, StringBuffer_t * sb, const L3ParserSettings_t * settings)
{
StringBuffer_appendChar(sb, '{');
@@ -959,9 +1019,11 @@
StringBuffer_append(sb, ", ");
}
ASTNode* child = node->getChild(c);
- if (child->getType() == AST_RELATIONAL_EQ && child->getNumChildren() == 2) {
+ std::string classname = child->getClass();
+ if (child->getType() == AST_RELATIONAL_EQ && child->getNumChildren() == 2 &&
+ classname != "assignment" && classname != "boolean"){
L3FormulaFormatter_visit(child, child->getChild(0), sb, settings);
- StringBuffer_append(sb, " : ");
+ StringBuffer_append(sb, ": ");
L3FormulaFormatter_visit(child, child->getChild(1), sb, settings);
}
else {
Modified: branches/libsbml-experimental-lucian/src/sbml/math/L3FormulaFormatter.h
===================================================================
--- branches/libsbml-experimental-lucian/src/sbml/math/L3FormulaFormatter.h 2020-01-09 15:03:00 UTC (rev 26267)
+++ branches/libsbml-experimental-lucian/src/sbml/math/L3FormulaFormatter.h 2020-01-16 21:03:29 UTC (rev 26268)
@@ -257,6 +257,18 @@
/**
+* Visits the given ASTNode_t as generic function where the first
+* child is the function itself, and the subsequent children are its
+* arguments. Formatted as 'child1(child2[, child3...])'.
+*/
+void
+L3FormulaFormatter_visitGenericApply( const ASTNode_t *parent,
+ const ASTNode_t *node,
+ StringBuffer_t *sb,
+ const L3ParserSettings_t *settings );
+
+
+/**
* Visits the given ASTNode_t as the function "log(10, x)" and in doing so,
* formats it as "log10(x)" (where x is any subexpression).
*/
@@ -290,6 +302,18 @@
/**
+* Visits the given ASTNode_t as a selector, and formats it either
+* as child1[child2] (the default) or as child1.child2, depending
+* on the class.
+*/
+void
+L3FormulaFormatter_visitPythonSelector( const ASTNode_t *parent,
+ const ASTNode_t *node,
+ StringBuffer_t *sb,
+ const L3ParserSettings_t *settings );
+
+
+/**
* Visits the given ASTNode_t and formats it as a set or dictionary. It
* determines whether the node is a dictionary in one of two ways: one,
* if its class is 'dictionary', or two, if all of its children are
Modified: branches/libsbml-experimental-lucian/src/sbml/math/test/TestL3PythonFormulaFormatter.cpp
===================================================================
--- branches/libsbml-experimental-lucian/src/sbml/math/test/TestL3PythonFormulaFormatter.cpp 2020-01-09 15:03:00 UTC (rev 26267)
+++ branches/libsbml-experimental-lucian/src/sbml/math/test/TestL3PythonFormulaFormatter.cpp 2020-01-16 21:03:29 UTC (rev 26268)
@@ -184,7 +184,7 @@
"x > -y",
"[x, y, 3]",
"{5, y, x + y}",
- "{t : 3, g : 5, h : 6**2}",
+ "{t: 3, g: 5, h: 6**2}",
""
};
Modified: branches/libsbml-experimental-lucian/src/sbml/packages/l3v2extendedmath/extension/L3v2extendedmathASTPlugin.cpp
===================================================================
--- branches/libsbml-experimental-lucian/src/sbml/packages/l3v2extendedmath/extension/L3v2extendedmathASTPlugin.cpp 2020-01-09 15:03:00 UTC (rev 26267)
+++ branches/libsbml-experimental-lucian/src/sbml/packages/l3v2extendedmath/extension/L3v2extendedmathASTPlugin.cpp 2020-01-16 21:03:29 UTC (rev 26268)
@@ -61,6 +61,16 @@
two.push_back(2);
ASTNodeValues_t node;
+
+ node.type = AST_APPLY_FUNCTION;
+ node.name = "";
+ node.csymbolURL = "";
+ node.isFunction = true;
+ node.allowedChildrenType = ALLOWED_CHILDREN_ATLEAST;
+ node.numAllowedChildren = one;
+
+ mPkgASTNodeValues.push_back(node);
+
node.type = AST_FUNCTION_MAX;
node.name = "max";
node.csymbolURL = "";
|
|
From: <fbe...@us...> - 2020-01-09 15:03:02
|
Revision: 26267
http://sourceforge.net/p/sbml/code/26267
Author: fbergmann
Date: 2020-01-09 15:03:00 +0000 (Thu, 09 Jan 2020)
Log Message:
-----------
- fix memory issues
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2020-01-09 15:02:12 UTC (rev 26266)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2020-01-09 15:03:00 UTC (rev 26267)
@@ -1893,7 +1893,8 @@
ss_msg << " with id '" << tc.getId() << "'";
}
ss_msg << " has a 'componentsLength' of '";
- ss_msg << tc.getComponentsLength() + "', instead of a value of '16'.";
+ ss_msg << tc.getComponentsLength();
+ ss_msg << "', instead of a value of '16'.";
msg = ss_msg.str();
inv(false);
}
@@ -2164,6 +2165,7 @@
break;
}
}
+ delete[] data;
inv(fail == false);
}
END_CONSTRAINT
@@ -2215,6 +2217,7 @@
}
borders.insert(border);
}
+ delete[] data;
inv(fail == false);
}
END_CONSTRAINT
@@ -2298,6 +2301,7 @@
break;
}
}
+ delete[] data;
inv(fail == false);
}
END_CONSTRAINT
@@ -2335,7 +2339,7 @@
pre(sf.getDataType() == SPATIAL_DATAKIND_FLOAT);
SampledField* sf_nc = const_cast<SampledField*>(&sf);
size_t len = sf_nc->getUncompressedLength();
- double* data = new double[len];
+ double* data;
sf_nc->getUncompressedData(data, len);
for (size_t d = 0; d < len; d++) {
double val = data[d];
@@ -2353,7 +2357,7 @@
break;
}
}
- delete[] data;
+ free(data);
inv(fail == false);
}
END_CONSTRAINT
@@ -2367,7 +2371,7 @@
pre(sf.getDataType() == SPATIAL_DATAKIND_UINT || sf.getDataType() == SPATIAL_DATAKIND_UINT8 || sf.getDataType() == SPATIAL_DATAKIND_UINT16 || sf.getDataType() == SPATIAL_DATAKIND_UINT32);
SampledField* sf_nc = const_cast<SampledField*>(&sf);
size_t len = sf_nc->getUncompressedLength();
- double* data = new double[len];
+ double* data;
sf_nc->getUncompressedData(data, len);
for (size_t d = 0; d < len; d++) {
double val = data[d];
@@ -2386,7 +2390,7 @@
break;
}
}
- delete[] data;
+ free(data);
inv(fail == false);
}
END_CONSTRAINT
@@ -2400,7 +2404,7 @@
pre(sf.getDataType() == SPATIAL_DATAKIND_INT || sf.getDataType() == SPATIAL_DATAKIND_UINT || sf.getDataType() == SPATIAL_DATAKIND_UINT8 || sf.getDataType() == SPATIAL_DATAKIND_UINT16 || sf.getDataType() == SPATIAL_DATAKIND_UINT32);
SampledField* sf_nc = const_cast<SampledField*>(&sf);
size_t len = sf_nc->getUncompressedLength();
- double* data = new double[len];
+ double* data;
sf_nc->getUncompressedData(data, len);
for (size_t d = 0; d < len; d++) {
double val = data[d];
@@ -2419,7 +2423,7 @@
break;
}
}
- delete[] data;
+ free(data);
inv(fail == false);
}
END_CONSTRAINT
|
|
From: <fbe...@us...> - 2020-01-09 15:02:13
|
Revision: 26266
http://sourceforge.net/p/sbml/code/26266
Author: fbergmann
Date: 2020-01-09 15:02:12 +0000 (Thu, 09 Jan 2020)
Log Message:
-----------
- fix when using namespaces
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/extension/test/TestPackage.cpp
Modified: branches/libsbml-experimental/src/sbml/extension/test/TestPackage.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/extension/test/TestPackage.cpp 2019-12-21 02:19:41 UTC (rev 26265)
+++ branches/libsbml-experimental/src/sbml/extension/test/TestPackage.cpp 2020-01-09 15:02:12 UTC (rev 26266)
@@ -82,7 +82,9 @@
"Test"
};
+LIBSBML_CPP_NAMESPACE_BEGIN
template class SBMLExtensionNamespaces<TestExtension>;
+LIBSBML_CPP_NAMESPACE_END
TestExtension::TestExtension ()
{
|
|
From: <luc...@us...> - 2019-12-21 02:19:44
|
Revision: 26265
http://sourceforge.net/p/sbml/code/26265
Author: luciansmith
Date: 2019-12-21 02:19:41 +0000 (Sat, 21 Dec 2019)
Log Message:
-----------
Set eol-style on new files.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221250-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221250-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221250-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221250-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221250-pass-00-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221704-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221704-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221706-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221706-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221706-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221707-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221707-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221707-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221708-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221708-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221708-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221905-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221905-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221906-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221906-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221908-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221908-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221908-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221908-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221908-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222104-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222104-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222104-pass-00-01.xml
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branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-05.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-05.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-06.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-05.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-06.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223405-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223405-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223605-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223605-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223607-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223607-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223752-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223752-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223752-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-05.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-pass-00-01.xml
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221250-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221250-fail-01-01.xml 2019-12-21 02:17:33 UTC (rev 26264)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221250-fail-01-01.xml 2019-12-21 02:19:41 UTC (rev 26265)
@@ -1,63 +1,63 @@
-<?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_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_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>
- </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: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:listOfGeometryDefinitions>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:numSamples2="1" spatial:numSamples3="1" spatial:samplesLength="0"/>
- </spatial:listOfSampledFields>
- </spatial:geometry>
- </model>
-</sbml>
-
+<?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_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_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>
+ </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: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:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:numSamples2="1" spatial:numSamples3="1" spatial:samplesLength="0"/>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Property changes on: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221250-fail-01-01.xml
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221250-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221250-pass-00-01.xml 2019-12-21 02:17:33 UTC (rev 26264)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221250-pass-00-01.xml 2019-12-21 02:19:41 UTC (rev 26265)
@@ -1,63 +1,63 @@
-<?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_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_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>
- </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:listOfGeometryDefinitions>
- <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
- <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="true" 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="true">
- <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:listOfGeometryDefinitions>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:numSamples2="1" spatial:numSamples3="1" spatial:samplesLength="0"/>
- </spatial:listOfSampledFields>
- </spatial:geometry>
- </model>
-</sbml>
-
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
+ <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="true" 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="true">
+ <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:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:numSamples2="1" spatial:numSamples3="1" spatial:samplesLength="0"/>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Property changes on: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221250-pass-00-01.xml
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221250-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221250-pass-00-02.xml 2019-12-21 02:17:33 UTC (rev 26264)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221250-pass-00-02.xml 2019-12-21 02:19:41 UTC (rev 26265)
@@ -1,63 +1,63 @@
-<?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_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_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>
- </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: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="true">
- <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:listOfGeometryDefinitions>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:numSamples2="1" spatial:numSamples3="1" spatial:samplesLength="0"/>
- </spatial:listOfSampledFields>
- </spatial:geometry>
- </model>
-</sbml>
-
+<?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_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_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>
+ </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: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 xmln...
[truncated message content] |
|
From: <luc...@us...> - 2019-12-21 02:17:36
|
Revision: 26264
http://sourceforge.net/p/sbml/code/26264
Author: luciansmith
Date: 2019-12-21 02:17:33 +0000 (Sat, 21 Dec 2019)
Log Message:
-----------
Add support and tests for spatial rules 23752-4. Also, fix old models that failed the new rules.
Modified Paths:
--------------
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/1221652-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221652-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221652-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221652-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221653-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221653-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221653-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221656-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221656-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-05.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-06.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-pass-00-01.xml
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223752-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223752-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223752-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-05.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-pass-00-03.xml
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-12-21 02:17:33 UTC (rev 26264)
@@ -2664,6 +2664,103 @@
END_CONSTRAINT
+// 1223752
+START_CONSTRAINT(SpatialGeometryCoordinateComponent1DisX, Geometry, geom)
+{
+ unsigned int naxes = geom.getNumCoordinateComponents();
+ pre(naxes == 1);
+ const CoordinateComponent* cc = geom.getCoordinateComponent(0);
+ pre(cc->isSetType());
+ pre(cc->getType() != SPATIAL_COORDINATEKIND_CARTESIAN_X);
+ stringstream ss_msg;
+ ss_msg << "The <geometry>";
+ if (geom.isSetId())
+ {
+ ss_msg << " with id '" << geom.getId() << "'";
+ }
+ ss_msg << " has only one child <coordinateComponents>, but its type is '";
+ ss_msg << cc->getTypeAsString() << "' instead of 'cartesianX'.";
+ msg = ss_msg.str();
+
+ inv(false);
+}
+END_CONSTRAINT
+
+
+// 1223753
+START_CONSTRAINT(SpatialGeometryCoordinateComponent2DisXY, Geometry, geom)
+{
+ unsigned int naxes = geom.getNumCoordinateComponents();
+ pre(naxes == 2);
+ const CoordinateComponent* cc1 = geom.getCoordinateComponent(0);
+ const CoordinateComponent* cc2 = geom.getCoordinateComponent(1);
+ pre(cc1->isSetType());
+ pre(cc2->isSetType());
+ CoordinateKind_t kind1 = cc1->getType();
+ CoordinateKind_t kind2 = cc2->getType();
+ std::set<CoordinateKind_t> kinds, rightkinds;
+ kinds.insert(kind1);
+ kinds.insert(kind2);
+ rightkinds.insert(SPATIAL_COORDINATEKIND_CARTESIAN_X);
+ rightkinds.insert(SPATIAL_COORDINATEKIND_CARTESIAN_Y);
+ pre(kinds != rightkinds);
+
+ stringstream ss_msg;
+ ss_msg << "The <geometry>";
+ if (geom.isSetId())
+ {
+ ss_msg << " with id '" << geom.getId() << "'";
+ }
+ ss_msg << " has two child <coordinateComponents>, but their two types are '";
+ ss_msg << cc1->getTypeAsString() << "' and '";
+ ss_msg << cc2->getTypeAsString() << "' instead of 'cartesianX' and 'cartesianY'.";
+ msg = ss_msg.str();
+
+ inv(false);
+}
+END_CONSTRAINT
+
+
+// 1223754
+START_CONSTRAINT(SpatialGeometryCoordinateComponent3DisXYZ, Geometry, geom)
+{
+ unsigned int naxes = geom.getNumCoordinateComponents();
+ pre(naxes == 3);
+ const CoordinateComponent* cc1 = geom.getCoordinateComponent(0);
+ const CoordinateComponent* cc2 = geom.getCoordinateComponent(1);
+ const CoordinateComponent* cc3 = geom.getCoordinateComponent(2);
+ pre(cc1->isSetType());
+ pre(cc2->isSetType());
+ pre(cc3->isSetType());
+ CoordinateKind_t kind1 = cc1->getType();
+ CoordinateKind_t kind2 = cc2->getType();
+ CoordinateKind_t kind3 = cc3->getType();
+ std::set<CoordinateKind_t> kinds, rightkinds;
+ kinds.insert(kind1);
+ kinds.insert(kind2);
+ kinds.insert(kind3);
+ rightkinds.insert(SPATIAL_COORDINATEKIND_CARTESIAN_X);
+ rightkinds.insert(SPATIAL_COORDINATEKIND_CARTESIAN_Y);
+ rightkinds.insert(SPATIAL_COORDINATEKIND_CARTESIAN_Z);
+ pre(kinds != rightkinds);
+
+ stringstream ss_msg;
+ ss_msg << "The <geometry>";
+ if (geom.isSetId())
+ {
+ ss_msg << " with id '" << geom.getId() << "'";
+ }
+ ss_msg << " has two child <coordinateComponents>, but their two types are '";
+ ss_msg << cc1->getTypeAsString() << "', '";
+ ss_msg << cc2->getTypeAsString() << "', and '";
+ ss_msg << cc3->getTypeAsString() << "', instead of 'cartesianX', 'cartesianY', and 'cartesianZ'.";
+ msg = ss_msg.str();
+
+ inv(false);
+}
+END_CONSTRAINT
+
+
// 122__
//START_CONSTRAINT(Spatial, Class, class)
//{
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-12-21 02:17:33 UTC (rev 26264)
@@ -135,6 +135,9 @@
addConstraint(new VConstraintBoundaryConditionSpatialBoundaryConditionBoundaryDomainTypeOrCoordinateBoundary(*this));
addConstraint(new VConstraintMixedGeometrySpatialMixedGeometryChildrenNotActive(*this));
addConstraint(new VConstraintGeometrySpatialGeometryLOCoordinateComponentsOneToThreeChildren(*this));
+addConstraint(new VConstraintGeometrySpatialGeometryCoordinateComponent1DisX(*this));
+addConstraint(new VConstraintGeometrySpatialGeometryCoordinateComponent2DisXY(*this));
+addConstraint(new VConstraintGeometrySpatialGeometryCoordinateComponent3DisXYZ(*this));
//Constraints defined in their own class ('global constraints')
addConstraint(new SpatialCompartmentMappingUnitSizesCheck(SpatialCompartmentMappingUnitSizesSum, *this));
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221652-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221652-fail-01-01.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221652-fail-01-01.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221652-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221652-fail-01-02.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221652-fail-01-02.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221652-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221652-fail-01-03.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221652-fail-01-03.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221652-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221652-pass-00-01.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221652-pass-00-01.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221653-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221653-fail-01-01.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221653-fail-01-01.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221653-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221653-fail-01-02.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221653-fail-01-02.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221653-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221653-pass-00-01.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221653-pass-00-01.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-fail-01-01.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-fail-01-01.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-fail-01-02.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-fail-01-02.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-fail-01-03.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-fail-01-03.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-fail-01-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-fail-01-04.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-fail-01-04.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-pass-00-01.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-pass-00-01.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-pass-00-02.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221655-pass-00-02.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221656-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221656-fail-01-01.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221656-fail-01-01.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221656-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221656-pass-00-01.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221656-pass-00-01.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-01.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-01.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-02.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-02.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-03.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-03.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-04.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-04.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-05.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-05.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-05.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-06.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-06.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-fail-01-06.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-pass-00-01.xml 2019-12-21 01:41:22 UTC (rev 26263)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221657-pass-00-01.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -7,7 +7,7 @@
<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_2" spatial:type="cartesianX">
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY">
<spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
<spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
</spatial:coordinateComponent>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223752-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223752-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223752-fail-01-01.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -0,0 +1,14 @@
+<?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="cartesianY" 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:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223752-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223752-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223752-fail-01-02.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -0,0 +1,14 @@
+<?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="cartesianZ" 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:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223752-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223752-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223752-pass-00-01.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -0,0 +1,14 @@
+<?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:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-01.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -0,0 +1,18 @@
+<?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_2" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-02.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -0,0 +1,18 @@
+<?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="cartesianY" 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_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:listOfCoordinateComponents>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-03.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -0,0 +1,18 @@
+<?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="cartesianY" 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_2" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-fail-01-04.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -0,0 +1,18 @@
+<?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_2" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-pass-00-01.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -0,0 +1,18 @@
+<?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_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:listOfCoordinateComponents>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-pass-00-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223753-pass-00-02.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -0,0 +1,18 @@
+<?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="cartesianY" 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_2" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-01.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -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: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_3" spatial:type="cartesianY" 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:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-02.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -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: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_3" spatial:type="cartesianX" 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:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-03.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -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:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianZ" 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_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>
+ </spatial:listOfCoordinateComponents>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-04.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -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:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianX" 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_3" spatial:type="cartesianX" 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:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-05.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-05.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223754-fail-00-05.xml 2019-12-21 02:17:33 UTC (rev 26264)
@@ -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/v...
[truncated message content] |
|
From: <luc...@us...> - 2019-12-21 01:41:24
|
Revision: 26263
http://sourceforge.net/p/sbml/code/26263
Author: luciansmith
Date: 2019-12-21 01:41:22 +0000 (Sat, 21 Dec 2019)
Log Message:
-----------
Add tests for spatial validation rule 23751. Also, remove 23750, as it was covered by this one.
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/1223751-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-pass-00-03.xml
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-12-21 01:22:39 UTC (rev 26262)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-12-21 01:41:22 UTC (rev 26263)
@@ -360,7 +360,6 @@
, SpatialGeometryLOAdjacentDomainsAllowedCoreAttributes = 1223715
, SpatialGeometryLOGeometryDefinitionsAllowedCoreAttributes = 1223716
, SpatialGeometryLOSampledFieldsAllowedCoreAttributes = 1223717
-, SpatialGeometryLOCoordinateComponentsRequired = 1223750
, SpatialGeometryLOCoordinateComponentsOneToThreeChildren = 1223751
, SpatialGeometryCoordinateComponent1DisX = 1223752
, SpatialGeometryCoordinateComponent2DisXY = 1223753
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-12-21 01:22:39 UTC (rev 26262)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-12-21 01:41:22 UTC (rev 26263)
@@ -3500,16 +3500,6 @@
}
},
- // 1223750
- { SpatialGeometryLOCoordinateComponentsRequired,
- "A <geometry> must have a <listOfCoordinateComponents>.",
- LIBSBML_CAT_GENERAL_CONSISTENCY,
- LIBSBML_SEV_ERROR,
- "A <geometry> must have a child <listOfCoordinateComponents> object.",
- { "L3V1 Spatial V1 Section"
- }
- },
-
// 1223751
{ SpatialGeometryLOCoordinateComponentsOneToThreeChildren,
"A <listOfCoordinateComponents> must have one to three children.",
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-12-21 01:22:39 UTC (rev 26262)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-12-21 01:41:22 UTC (rev 26263)
@@ -2644,6 +2644,26 @@
END_CONSTRAINT
+// 1223751
+START_CONSTRAINT(SpatialGeometryLOCoordinateComponentsOneToThreeChildren, Geometry, geom)
+{
+ unsigned int naxes = geom.getNumCoordinateComponents();
+ pre(naxes < 1 || naxes>3);
+ stringstream ss_msg;
+ ss_msg << "The <geometry>";
+ if (geom.isSetId())
+ {
+ ss_msg << " with id '" << geom.getId() << "'";
+ }
+ ss_msg << " has " << naxes << " child <coordinateComponents>, but must have 1 to 3 instead.";
+ msg = ss_msg.str();
+
+
+ inv(false);
+}
+END_CONSTRAINT
+
+
// 122__
//START_CONSTRAINT(Spatial, Class, class)
//{
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-12-21 01:22:39 UTC (rev 26262)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-12-21 01:41:22 UTC (rev 26263)
@@ -134,6 +134,7 @@
addConstraint(new VConstraintGeometrySpatialOneGeometryDefinitionMustBeActive(*this));
addConstraint(new VConstraintBoundaryConditionSpatialBoundaryConditionBoundaryDomainTypeOrCoordinateBoundary(*this));
addConstraint(new VConstraintMixedGeometrySpatialMixedGeometryChildrenNotActive(*this));
+addConstraint(new VConstraintGeometrySpatialGeometryLOCoordinateComponentsOneToThreeChildren(*this));
//Constraints defined in their own class ('global constraints')
addConstraint(new SpatialCompartmentMappingUnitSizesCheck(SpatialCompartmentMappingUnitSizesSum, *this));
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-fail-01-01.xml 2019-12-21 01:41:22 UTC (rev 26263)
@@ -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: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_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>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_4" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_7" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_8" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-fail-01-02.xml 2019-12-21 01:41:22 UTC (rev 26263)
@@ -0,0 +1,7 @@
+<?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"/>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-pass-00-01.xml 2019-12-21 01:41:22 UTC (rev 26263)
@@ -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: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_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>
+ </spatial:listOfCoordinateComponents>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-pass-00-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-pass-00-02.xml 2019-12-21 01:41:22 UTC (rev 26263)
@@ -0,0 +1,18 @@
+<?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_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:listOfCoordinateComponents>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-pass-00-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-pass-00-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223751-pass-00-03.xml 2019-12-21 01:41:22 UTC (rev 26263)
@@ -0,0 +1,14 @@
+<?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:geometry>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2019-12-21 01:22:41
|
Revision: 26262
http://sourceforge.net/p/sbml/code/26262
Author: luciansmith
Date: 2019-12-21 01:22:39 +0000 (Sat, 21 Dec 2019)
Log Message:
-----------
Add support and tests for spatial rule 23850.
Modified Paths:
--------------
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/1223850-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-pass-00-01.xml
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-12-21 00:58:10 UTC (rev 26261)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-12-21 01:22:39 UTC (rev 26262)
@@ -2589,6 +2589,36 @@
END_CONSTRAINT
+// 1223850
+START_CONSTRAINT(SpatialMixedGeometryChildrenNotActive, MixedGeometry, mg)
+{
+ bool fail = false;
+ pre(mg.getNumGeometryDefinitions() > 0);
+ for (unsigned long gdn = 0; gdn < mg.getNumGeometryDefinitions(); gdn++)
+ {
+ const GeometryDefinition* gd = mg.getGeometryDefinition(gdn);
+ if (gd->getIsActive() == true)
+ {
+ msg = "A <mixedGeometry>";
+ if (mg.isSetId())
+ {
+ msg += " with the id '" + mg.getId() + "'";
+ }
+ msg += " has a child <" + gd->getElementName() + ">";
+ if (gd->isSetId())
+ {
+ msg += " with the id '" + gd->getId() + "'";
+ }
+ msg += " with an 'isActive' value of 'true'.";
+ fail = true;
+ break;
+ }
+ }
+ inv(fail == false);
+}
+END_CONSTRAINT
+
+
// 1223650
START_CONSTRAINT(SpatialBoundaryConditionBoundaryDomainTypeOrCoordinateBoundary, BoundaryCondition, bc)
{
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-12-21 00:58:10 UTC (rev 26261)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-12-21 01:22:39 UTC (rev 26262)
@@ -133,6 +133,7 @@
addConstraint(new VConstraintBoundaryConditionSpatialBoundaryConditionCoordinateBoundaryMustBeBoundary(*this));
addConstraint(new VConstraintGeometrySpatialOneGeometryDefinitionMustBeActive(*this));
addConstraint(new VConstraintBoundaryConditionSpatialBoundaryConditionBoundaryDomainTypeOrCoordinateBoundary(*this));
+addConstraint(new VConstraintMixedGeometrySpatialMixedGeometryChildrenNotActive(*this));
//Constraints defined in their own class ('global constraints')
addConstraint(new SpatialCompartmentMappingUnitSizesCheck(SpatialCompartmentMappingUnitSizesSum, *this));
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-fail-01-01.xml 2019-12-21 01:22:39 UTC (rev 26262)
@@ -0,0 +1,62 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:mixedGeometry spatial:id="geometryDefinition_4" spatial:isActive="true">
+ <spatial:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
+ <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="true" 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:listOfGeometryDefinitions>
+ <spatial:listOfOrdinalMappings>
+ <spatial:ordinalMapping spatial:geometryDefinition="geometryDefinition_1" spatial:ordinal="0"/>
+ <spatial:ordinalMapping spatial:geometryDefinition="geometryDefinition_2" spatial:ordinal="1"/>
+ </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="0"/>
+ </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>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-fail-01-02.xml 2019-12-21 01:22:39 UTC (rev 26262)
@@ -0,0 +1,62 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:mixedGeometry spatial:id="geometryDefinition_4" spatial:isActive="true">
+ <spatial:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
+ <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:listOfGeometryDefinitions>
+ <spatial:listOfOrdinalMappings>
+ <spatial:ordinalMapping spatial:geometryDefinition="geometryDefinition_1" spatial:ordinal="0"/>
+ <spatial:ordinalMapping spatial:geometryDefinition="geometryDefinition_2" spatial:ordinal="1"/>
+ </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="0"/>
+ </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>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-fail-01-03.xml 2019-12-21 01:22:39 UTC (rev 26262)
@@ -0,0 +1,62 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:mixedGeometry spatial:id="geometryDefinition_4" spatial:isActive="true">
+ <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="true" 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:listOfGeometryDefinitions>
+ <spatial:listOfOrdinalMappings>
+ <spatial:ordinalMapping spatial:geometryDefinition="geometryDefinition_1" spatial:ordinal="0"/>
+ <spatial:ordinalMapping spatial:geometryDefinition="geometryDefinition_2" spatial:ordinal="1"/>
+ </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="0"/>
+ </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>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223850-pass-00-01.xml 2019-12-21 01:22:39 UTC (rev 26262)
@@ -0,0 +1,62 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:mixedGeometry spatial:id="geometryDefinition_4" spatial:isActive="true">
+ <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:listOfGeometryDefinitions>
+ <spatial:listOfOrdinalMappings>
+ <spatial:ordinalMapping spatial:geometryDefinition="geometryDefinition_1" spatial:ordinal="0"/>
+ <spatial:ordinalMapping spatial:geometryDefinition="geometryDefinition_2" spatial:ordinal="1"/>
+ </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="0"/>
+ </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>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2019-12-21 00:58:13
|
Revision: 26261
http://sourceforge.net/p/sbml/code/26261
Author: luciansmith
Date: 2019-12-21 00:58:10 +0000 (Sat, 21 Dec 2019)
Log Message:
-----------
Add support and tests for spatial rule 23650. Also fix all the old models that failed this rule.
Modified Paths:
--------------
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/1220501-fail-01-03.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-01-08.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-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223604-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223604-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223605-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223605-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223607-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223607-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-05.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-06.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-07.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-08.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-09.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-10.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-11.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-12.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-13.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-14.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-15.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-16.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-17.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-18.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-02-19.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-02-20.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-02-21.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-pass-00-03.xml
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-pass-00-02.xml
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-12-21 00:58:10 UTC (rev 26261)
@@ -2550,7 +2550,7 @@
// 1223606
START_CONSTRAINT(SpatialBoundaryConditionCoordinateBoundaryMustBeBoundary, BoundaryCondition, bc)
{
- pre(bc.isSetVariable());
+ pre(bc.isSetCoordinateBoundary());
string boundary = bc.getCoordinateBoundary();
SpatialModelPlugin *mplug = (SpatialModelPlugin*)(m.getPlugin("spatial"));
pre(mplug != NULL);
@@ -2589,6 +2589,31 @@
END_CONSTRAINT
+// 1223650
+START_CONSTRAINT(SpatialBoundaryConditionBoundaryDomainTypeOrCoordinateBoundary, BoundaryCondition, bc)
+{
+ bool fail = false;
+
+ msg = "A <boundaryCondition>";
+ if (bc.isSetId()) {
+ msg += " with the id '" + bc.getId() + "'";
+ }
+ if (bc.isSetBoundaryDomainType() && bc.isSetCoordinateBoundary())
+ {
+ msg += " has a value of '" + bc.getBoundaryDomainType() + "' for its 'boundaryDomainType', and a value of '" + bc.getCoordinateBoundary() + "' for its 'coordinateBoundary'. It must instead have one or the other.";
+ fail = true;
+ }
+ else if (!bc.isSetBoundaryDomainType() && !bc.isSetCoordinateBoundary())
+ {
+ msg += " does not have a value for its 'boundaryDomainType' nor its 'coordinateBoundary' attributes. It must have one or the other.";
+ fail = true;
+ }
+
+ inv(fail == false);
+}
+END_CONSTRAINT
+
+
// 122__
//START_CONSTRAINT(Spatial, Class, class)
//{
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-12-21 00:58:10 UTC (rev 26261)
@@ -132,6 +132,7 @@
addConstraint(new VConstraintDiffusionCoefficientSpatialDiffusionCoefficientVariableMustBeSpecies(*this));
addConstraint(new VConstraintBoundaryConditionSpatialBoundaryConditionCoordinateBoundaryMustBeBoundary(*this));
addConstraint(new VConstraintGeometrySpatialOneGeometryDefinitionMustBeActive(*this));
+addConstraint(new VConstraintBoundaryConditionSpatialBoundaryConditionBoundaryDomainTypeOrCoordinateBoundary(*this));
//Constraints defined in their own class ('global constraints')
addConstraint(new SpatialCompartmentMappingUnitSizesCheck(SpatialCompartmentMappingUnitSizesSum, *this));
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 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-03.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,8 +68,8 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
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 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-06.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -69,7 +69,7 @@
<listOfParameters>
<parameter constant="false" id="id_3">
<spatial:spatialSymbolReference spatial:spatialRef="coordinateComponent_2"/>
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
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 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-08.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -69,7 +69,7 @@
<listOfParameters>
<parameter constant="false" id="id_3">
<spatial:advectionCoefficient spatial:coordinate="cartesianX" spatial:variable="species_1"/>
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
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 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-fail-01-10.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,7 +68,7 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
<spatial:diffusionCoefficient spatial:coordinateReference1="cartesianX" spatial:coordinateReference2="cartesianY" spatial:type="tensor" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
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 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220501-pass-00-03.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,7 +68,7 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223604-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223604-fail-01-01.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223604-fail-01-01.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,7 +68,7 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_2"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_2"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223604-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223604-pass-00-01.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223604-pass-00-01.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,7 +68,7 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223605-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223605-fail-01-01.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223605-fail-01-01.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,7 +68,7 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Kramer" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Kramer" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223605-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223605-pass-00-01.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223605-pass-00-01.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,7 +68,7 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-01.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-01.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,7 +68,7 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_42" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_42" spatial:type="Neumann" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-02.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-02.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,7 +68,7 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="coordinateComponent_1" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="coordinateComponent_1" spatial:type="Neumann" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-03.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-03.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,7 +68,7 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="id_3" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="id_3" spatial:type="Neumann" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-pass-00-01.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-pass-00-01.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,7 +68,7 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223607-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223607-fail-01-01.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223607-fail-01-01.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -32,7 +32,7 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainNotType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:boundaryDomainType="domainNotType_1" spatial:type="Neumann" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223607-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223607-pass-00-01.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223607-pass-00-01.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -32,7 +32,7 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:type="Neumann" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-fail-01-01.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -0,0 +1,76 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
+ <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="true" 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="true">
+ <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: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="0"/>
+ </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="species_1" spatial:isSpatial="false"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="id_3">
+ <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ </parameter>
+ </listOfParameters>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-fail-01-02.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -0,0 +1,76 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
+ <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="true" 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="true">
+ <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: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="0"/>
+ </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="species_1" spatial:isSpatial="false"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="id_3">
+ <spatial:boundaryCondition spatial:type="Neumann" spatial:variable="species_1"/>
+ </parameter>
+ </listOfParameters>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-pass-00-01.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -0,0 +1,76 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
+ <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="true" 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="true">
+ <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: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="0"/>
+ </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="species_1" spatial:isSpatial="false"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="id_3">
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ </parameter>
+ </listOfParameters>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-pass-00-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223650-pass-00-02.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -0,0 +1,76 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
+ <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="true" 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="true">
+ <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: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="0"/>
+ </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="species_1" spatial:isSpatial="false"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="id_3">
+ <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:type="Neumann" spatial:variable="species_1"/>
+ </parameter>
+ </listOfParameters>
+ </model>
+</sbml>
+
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-01.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-01.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,10 +68,10 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
</parameter>
<parameter constant="false" id="id_4">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Dirichlet" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Dirichlet" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-02.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-02.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,10 +68,10 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
</parameter>
<parameter constant="false" id="id_4">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Robin_sum" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Robin_sum" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-03.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-03.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,10 +68,10 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
</parameter>
<parameter constant="false" id="id_4">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Robin_inwardNormalGradientCoefficient" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Robin_inwardNormalGradientCoefficient" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-04.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-04.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,10 +68,10 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
</parameter>
<parameter constant="false" id="id_4">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Robin_valueCoefficient" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Robin_valueCoefficient" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-05.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-05.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-05.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,10 +68,10 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Dirichlet" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Dirichlet" spatial:variable="species_1"/>
</parameter>
<parameter constant="false" id="id_4">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-06.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-06.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-06.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,10 +68,10 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Dirichlet" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Dirichlet" spatial:variable="species_1"/>
</parameter>
<parameter constant="false" id="id_4">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Robin_sum" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Robin_sum" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-07.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-07.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-07.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,10 +68,10 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Dirichlet" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Dirichlet" spatial:variable="species_1"/>
</parameter>
<parameter constant="false" id="id_4">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Robin_valueCoefficient" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Robin_valueCoefficient" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-08.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-08.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-08.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,10 +68,10 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Dirichlet" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Dirichlet" spatial:variable="species_1"/>
</parameter>
<parameter constant="false" id="id_4">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Robin_inwardNormalGradientCoefficient" spatial:variable="species_1"/>
+ <spatial:boundaryCondition spatial:coordinateBoundary="boundary_2" spatial:type="Robin_inwardNormalGradientCoefficient" spatial:variable="species_1"/>
</parameter>
</listOfParameters>
</model>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-09.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-09.xml 2019-12-20 23:59:19 UTC (rev 26260)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223651-fail-01-09.xml 2019-12-21 00:58:10 UTC (rev 26261)
@@ -68,16 +68,16 @@
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
- <spatial:boundaryCondition spatial:boundaryDomainType="domainTyp...
[truncated message content] |
|
From: <luc...@us...> - 2019-12-20 23:59:22
|
Revision: 26260
http://sourceforge.net/p/sbml/code/26260
Author: luciansmith
Date: 2019-12-20 23:59:19 +0000 (Fri, 20 Dec 2019)
Log Message:
-----------
Add support and tests for spatial rule 23606. Also change 'with that ID' to 'with that id', since 'ID' might be construed as being the XML ID.
Modified Paths:
--------------
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/1223606-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-pass-00-01.xml
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-12-20 23:39:45 UTC (rev 26259)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-12-20 23:59:19 UTC (rev 26260)
@@ -720,7 +720,7 @@
const SBase* ref = model->getElementBySId(ssr.getSpatialRef());
if (ref == NULL) {
fail = true;
- msg += ", but no object with that ID could be found.";
+ msg += ", but no object with that id could be found.";
}
else {
switch (ref->getTypeCode()) {
@@ -2439,7 +2439,7 @@
if (sv.isSetId()) {
msg += " with the id '" + sv.getId() + "'";
}
- msg += " has a value of '" + domaintype + "' for its 'domainType', but the <geometry> does not contain a <domainType> with that ID.";
+ msg += " has a value of '" + domaintype + "' for its 'domainType', but the <geometry> does not contain a <domainType> with that id.";
inv(false);
}
@@ -2460,7 +2460,7 @@
if (av.isSetId()) {
msg += " with the id '" + av.getId() + "'";
}
- msg += " has a value of '" + domaintype + "' for its 'domainType', but the <geometry> does not contain a <domainType> with that ID.";
+ msg += " has a value of '" + domaintype + "' for its 'domainType', but the <geometry> does not contain a <domainType> with that id.";
inv(false);
}
@@ -2481,7 +2481,7 @@
if (po.isSetId()) {
msg += " with the id '" + po.getId() + "'";
}
- msg += " has a value of '" + domaintype + "' for its 'domainType', but the <geometry> does not contain a <domainType> with that ID.";
+ msg += " has a value of '" + domaintype + "' for its 'domainType', but the <geometry> does not contain a <domainType> with that id.";
inv(false);
}
@@ -2502,7 +2502,7 @@
if (csgo.isSetId()) {
msg += " with the id '" + csgo.getId() + "'";
}
- msg += " has a value of '" + domaintype + "' for its 'domainType', but the <geometry> does not contain a <domainType> with that ID.";
+ msg += " has a value of '" + domaintype + "' for its 'domainType', but the <geometry> does not contain a <domainType> with that id.";
inv(false);
}
@@ -2523,7 +2523,7 @@
if (bc.isSetId()) {
msg += " with the id '" + bc.getId() + "'";
}
- msg += " has a value of '" + domaintype + "' for its 'boundaryDomainType', but the <geometry> does not contain a <domainType> with that ID.";
+ msg += " has a value of '" + domaintype + "' for its 'boundaryDomainType', but the <geometry> does not contain a <domainType> with that id.";
inv(false);
}
@@ -2540,7 +2540,7 @@
if (dc.isSetId()) {
msg += " with the id '" + dc.getId() + "'";
}
- msg += " has a value of '" + variable + "' for its 'variable', but the model does not contain a <species> with that ID.";
+ msg += " has a value of '" + variable + "' for its 'variable', but the model does not contain a <species> with that id.";
inv(false);
}
@@ -2547,6 +2547,33 @@
END_CONSTRAINT
+// 1223606
+START_CONSTRAINT(SpatialBoundaryConditionCoordinateBoundaryMustBeBoundary, BoundaryCondition, bc)
+{
+ pre(bc.isSetVariable());
+ string boundary = bc.getCoordinateBoundary();
+ SpatialModelPlugin *mplug = (SpatialModelPlugin*)(m.getPlugin("spatial"));
+ pre(mplug != NULL);
+ Geometry* geom = mplug->getGeometry();
+ pre(geom != NULL);
+ for (unsigned long cc = 0; cc < geom->getNumCoordinateComponents(); cc++)
+ {
+ const CoordinateComponent* coord = geom->getCoordinateComponent(cc);
+ if (coord->isSetBoundaryMax()) {
+ pre(coord->getBoundaryMax()->getId() != boundary);
+ }
+ }
+ msg = "A <boundaryCondition>";
+ if (bc.isSetId()) {
+ msg += " with the id '" + bc.getId() + "'";
+ }
+ msg += " has a value of '" + boundary+ "' for its 'coordinateBoundary', but the <geometry> does not contain a <boundaryMax> or <boundaryMin> with that id.";
+
+ inv(false);
+}
+END_CONSTRAINT
+
+
// 1221250
START_CONSTRAINT(SpatialOneGeometryDefinitionMustBeActive, Geometry, g)
{
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-12-20 23:39:45 UTC (rev 26259)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-12-20 23:59:19 UTC (rev 26260)
@@ -129,8 +129,9 @@
addConstraint(new VConstraintParametricObjectSpatialParametricObjectDomainTypeMustBeDomainType(*this));
addConstraint(new VConstraintCSGObjectSpatialCSGObjectDomainTypeMustBeDomainType(*this));
addConstraint(new VConstraintBoundaryConditionSpatialBoundaryConditionBoundaryDomainTypeMustBeDomainType(*this));
+addConstraint(new VConstraintDiffusionCoefficientSpatialDiffusionCoefficientVariableMustBeSpecies(*this));
+addConstraint(new VConstraintBoundaryConditionSpatialBoundaryConditionCoordinateBoundaryMustBeBoundary(*this));
addConstraint(new VConstraintGeometrySpatialOneGeometryDefinitionMustBeActive(*this));
-addConstraint(new VConstraintDiffusionCoefficientSpatialDiffusionCoefficientVariableMustBeSpecies(*this));
//Constraints defined in their own class ('global constraints')
addConstraint(new SpatialCompartmentMappingUnitSizesCheck(SpatialCompartmentMappingUnitSizesSum, *this));
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-01.xml 2019-12-20 23:59:19 UTC (rev 26260)
@@ -0,0 +1,76 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
+ <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="true" 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="true">
+ <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: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="0"/>
+ </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="species_1" spatial:isSpatial="false"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="id_3">
+ <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_42" spatial:type="Neumann" spatial:variable="species_1"/>
+ </parameter>
+ </listOfParameters>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-02.xml 2019-12-20 23:59:19 UTC (rev 26260)
@@ -0,0 +1,76 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
+ <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="true" 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="true">
+ <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: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="0"/>
+ </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="species_1" spatial:isSpatial="false"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="id_3">
+ <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="coordinateComponent_1" spatial:type="Neumann" spatial:variable="species_1"/>
+ </parameter>
+ </listOfParameters>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-fail-01-03.xml 2019-12-20 23:59:19 UTC (rev 26260)
@@ -0,0 +1,76 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
+ <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="true" 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="true">
+ <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: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="0"/>
+ </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="species_1" spatial:isSpatial="false"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="id_3">
+ <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="id_3" spatial:type="Neumann" spatial:variable="species_1"/>
+ </parameter>
+ </listOfParameters>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223606-pass-00-01.xml 2019-12-20 23:59:19 UTC (rev 26260)
@@ -0,0 +1,76 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
+ <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="true" 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="true">
+ <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: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="0"/>
+ </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="species_1" spatial:isSpatial="false"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="id_3">
+ <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ </parameter>
+ </listOfParameters>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2019-12-20 23:39:47
|
Revision: 26259
http://sourceforge.net/p/sbml/code/26259
Author: luciansmith
Date: 2019-12-20 23:39:45 +0000 (Fri, 20 Dec 2019)
Log Message:
-----------
Add tests for spatial validation rule 23605.
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223605-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223605-pass-00-01.xml
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223605-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223605-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223605-fail-01-01.xml 2019-12-20 23:39:45 UTC (rev 26259)
@@ -0,0 +1,76 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
+ <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="true" 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="true">
+ <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: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="0"/>
+ </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="species_1" spatial:isSpatial="false"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="id_3">
+ <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Kramer" spatial:variable="species_1"/>
+ </parameter>
+ </listOfParameters>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223605-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223605-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223605-pass-00-01.xml 2019-12-20 23:39:45 UTC (rev 26259)
@@ -0,0 +1,76 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
+ <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="true" 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="true">
+ <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: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="0"/>
+ </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="species_1" spatial:isSpatial="false"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="id_3">
+ <spatial:boundaryCondition spatial:boundaryDomainType="domainType_1" spatial:coordinateBoundary="boundary_2" spatial:type="Neumann" spatial:variable="species_1"/>
+ </parameter>
+ </listOfParameters>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2019-12-20 23:34:12
|
Revision: 26258
http://sourceforge.net/p/sbml/code/26258
Author: luciansmith
Date: 2019-12-20 23:34:10 +0000 (Fri, 20 Dec 2019)
Log Message:
-----------
Add tests for spatial validation rule 23405.
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223405-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223405-pass-00-01.xml
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223405-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223405-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223405-fail-01-01.xml 2019-12-20 23:34:10 UTC (rev 26258)
@@ -0,0 +1,76 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
+ <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="true" 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="true">
+ <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: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="0"/>
+ </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="species_1" spatial:isSpatial="true"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="id_3">
+ <spatial:diffusionCoefficient spatial:type="isomorphic" spatial:variable="species_1"/>
+ </parameter>
+ </listOfParameters>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223405-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223405-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223405-pass-00-01.xml 2019-12-20 23:34:10 UTC (rev 26258)
@@ -0,0 +1,76 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
+ <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="true" 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="true">
+ <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: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="0"/>
+ </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="species_1" spatial:isSpatial="true"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="id_3">
+ <spatial:diffusionCoefficient spatial:type="isotropic" spatial:variable="species_1"/>
+ </parameter>
+ </listOfParameters>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2019-12-20 23:31:52
|
Revision: 26257
http://sourceforge.net/p/sbml/code/26257
Author: luciansmith
Date: 2019-12-20 23:31:50 +0000 (Fri, 20 Dec 2019)
Log Message:
-----------
Add support and tests for spatial rule 23404. Also fix all the old models that failed this rule.
Modified Paths:
--------------
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/1220401-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220401-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220401-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220402-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220402-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-fail-01-02.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/1220601-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220601-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220601-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220602-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220602-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220650-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220650-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220650-pass-00-02.xml
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
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
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223450-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223450-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223450-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223450-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223451-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223451-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223451-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223451-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223452-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223452-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223452-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223452-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223454-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223454-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223455-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223455-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223455-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223456-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223456-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223456-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223456-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223456-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223457-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223457-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223457-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223457-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223457-fail-01-05.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223457-fail-01-06.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223457-fail-01-07.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223457-fail-01-08.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223457-fail-01-09.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223457-fail-01-10.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223457-fail-01-11.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223457-fail-01-12.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223457-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223457-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223457-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223457-pass-00-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223457-pass-00-05.xml
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-pass-00-01.xml
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-12-20 23:31:50 UTC (rev 26257)
@@ -2530,6 +2530,23 @@
END_CONSTRAINT
+// 1223404
+START_CONSTRAINT(SpatialDiffusionCoefficientVariableMustBeSpecies, DiffusionCoefficient, dc)
+{
+ pre(dc.isSetVariable());
+ string variable = dc.getVariable();
+ pre(m.getSpecies(variable)==NULL);
+ msg = "A <diffusionCoefficient>";
+ if (dc.isSetId()) {
+ msg += " with the id '" + dc.getId() + "'";
+ }
+ msg += " has a value of '" + variable + "' for its 'variable', but the model does not contain a <species> with that ID.";
+
+ inv(false);
+}
+END_CONSTRAINT
+
+
// 1221250
START_CONSTRAINT(SpatialOneGeometryDefinitionMustBeActive, Geometry, g)
{
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-12-20 23:31:50 UTC (rev 26257)
@@ -130,6 +130,7 @@
addConstraint(new VConstraintCSGObjectSpatialCSGObjectDomainTypeMustBeDomainType(*this));
addConstraint(new VConstraintBoundaryConditionSpatialBoundaryConditionBoundaryDomainTypeMustBeDomainType(*this));
addConstraint(new VConstraintGeometrySpatialOneGeometryDefinitionMustBeActive(*this));
+addConstraint(new VConstraintDiffusionCoefficientSpatialDiffusionCoefficientVariableMustBeSpecies(*this));
//Constraints defined in their own class ('global constraints')
addConstraint(new SpatialCompartmentMappingUnitSizesCheck(SpatialCompartmentMappingUnitSizesSum, *this));
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220401-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220401-fail-01-01.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220401-fail-01-01.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -5,7 +5,7 @@
<compartment constant="false" id="compartment"/>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:foo="someString" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:foo="someString" spatial:isSpatial="false"/>
</listOfSpecies>
</model>
</sbml>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220401-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220401-pass-00-01.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220401-pass-00-01.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -5,7 +5,7 @@
<compartment constant="false" id="compartment"/>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
</model>
</sbml>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220401-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220401-pass-00-02.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220401-pass-00-02.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -5,7 +5,7 @@
<compartment constant="false" id="compartment"/>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1"/>
</listOfSpecies>
</model>
</sbml>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220402-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220402-fail-01-01.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220402-fail-01-01.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -5,7 +5,7 @@
<compartment constant="false" id="compartment"/>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="someString"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="someString"/>
</listOfSpecies>
</model>
</sbml>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220402-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220402-pass-00-01.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220402-pass-00-01.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -5,7 +5,7 @@
<compartment constant="false" id="compartment"/>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
</model>
</sbml>
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 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220450-fail-01-01.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -40,7 +40,7 @@
<compartment constant="false" id="compartment"/>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="true"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="true"/>
</listOfSpecies>
</model>
</sbml>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220450-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220450-fail-01-02.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220450-fail-01-02.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -5,7 +5,7 @@
<compartment constant="false" id="compartment"/>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="true"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="true"/>
</listOfSpecies>
</model>
</sbml>
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 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220450-pass-00-01.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -42,7 +42,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="true"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="true"/>
</listOfSpecies>
</model>
</sbml>
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220601-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220601-fail-01-01.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220601-fail-01-01.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -7,7 +7,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfReactions>
<reaction id="J0" reversible="false" fast="false">
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220601-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220601-fail-01-02.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220601-fail-01-02.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -7,7 +7,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfReactions>
<reaction id="J0" reversible="false" fast="false" spatial:isLocal="true" spatial:foo="x" compartment="compartment">
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220601-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220601-pass-00-01.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220601-pass-00-01.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -7,7 +7,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfReactions>
<reaction id="J0" reversible="false" fast="false" spatial:isLocal="false">
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220602-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220602-fail-01-01.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220602-fail-01-01.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -7,7 +7,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfReactions>
<reaction id="J0" reversible="false" fast="false" spatial:isLocal="anything">
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220602-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220602-pass-00-01.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220602-pass-00-01.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -7,7 +7,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfReactions>
<reaction id="J0" reversible="false" fast="false" spatial:isLocal="true" compartment="compartment">
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220650-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220650-fail-01-01.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220650-fail-01-01.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -6,7 +6,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220650-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220650-pass-00-01.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220650-pass-00-01.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -6,7 +6,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220650-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220650-pass-00-02.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1220650-pass-00-02.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -6,7 +6,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
Modified: 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-01-01.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-fail-01-01.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -64,7 +64,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
Modified: 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-01-02.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-fail-01-02.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -64,7 +64,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
Modified: 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-fail-01-03.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-fail-01-03.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -64,7 +64,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
Modified: 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-00-01.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-pass-00-01.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -64,7 +64,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
Modified: 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-00-02.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-pass-00-02.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -64,7 +64,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
Modified: 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-00-03.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-pass-00-03.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -64,7 +64,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="true" id="id_3">
Modified: 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-00-04.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-pass-00-04.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -64,7 +64,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
Modified: 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-00-05.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-pass-00-05.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -64,7 +64,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-pass-00-06.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-pass-00-06.xml 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223304-pass-00-06.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -64,7 +64,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
Modified: 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 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223350-fail-01-01.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -64,7 +64,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
Modified: 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 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223350-fail-02-02.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -64,7 +64,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
Modified: 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 2019-12-20 23:13:22 UTC (rev 26256)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223350-pass-00-01.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -64,7 +64,7 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
- <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="id_2" spatial:isSpatial="false"/>
+ <species boundaryCondition="false" compartment="compartment" constant="false" hasOnlySubstanceUnits="false" id="species_1" spatial:isSpatial="false"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="false" id="id_3">
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-fail-01-01.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -0,0 +1,76 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
+ <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="true" 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="true">
+ <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: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="0"/>
+ </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="species_1" spatial:isSpatial="true"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="id_3">
+ <spatial:diffusionCoefficient spatial:type="isotropic" spatial:variable="compartment"/>
+ </parameter>
+ </listOfParameters>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-fail-01-02.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -0,0 +1,76 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
+ <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="true" 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="true">
+ <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: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="0"/>
+ </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="species_1" spatial:isSpatial="true"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="id_3">
+ <spatial:diffusionCoefficient spatial:type="isotropic" spatial:variable="id_3"/>
+ </parameter>
+ </listOfParameters>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-fail-01-03.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -0,0 +1,76 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:analyticGeometry spatial:id="geometryDefinition_1" spatial:isActive="true">
+ <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="true" 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="true">
+ <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: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="0"/>
+ </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="species_1" spatial:isSpatial="true"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="id_3">
+ <spatial:diffusionCoefficient spatial:type="isotropic" spatial:variable="id_234"/>
+ </parameter>
+ </listOfParameters>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223404-pass-00-01.xml 2019-12-20 23:31:50 UTC (rev 26257)
@@ -0,0 +1,76 @@
+<?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_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_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>
+ </spatial:listOfCoordinateComponent...
[truncated message content] |
|
From: <luc...@us...> - 2019-12-20 23:13:23
|
Revision: 26256
http://sourceforge.net/p/sbml/code/26256
Author: luciansmith
Date: 2019-12-20 23:13:22 +0000 (Fri, 20 Dec 2019)
Log Message:
-----------
Add some more tests for spatial validation rule 23253, and remove spatial validation rules 23206 and 23207, as they are supplanted by the more restrictive 23253.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGSetOperator.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-05.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-06.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-pass-00-02.xml
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGSetOperator.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGSetOperator.cpp 2019-12-20 22:39:27 UTC (rev 26255)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGSetOperator.cpp 2019-12-20 23:13:22 UTC (rev 26256)
@@ -1506,7 +1506,7 @@
msg += " is '" + mComplementA + "', which does not conform to the "
"syntax.";
log->logPackageError("spatial",
- SpatialCSGSetOperatorComplementAMustBeCSGNode, pkgVersion, level,
+ SpatialCSGSetOperatorComplementsMustReferenceChildren, pkgVersion, level,
version, msg, getLine(), getColumn());
}
}
@@ -1535,7 +1535,7 @@
msg += " is '" + mComplementB + "', which does not conform to the "
"syntax.";
log->logPackageError("spatial",
- SpatialCSGSetOperatorComplementBMustBeCSGNode, pkgVersion, level,
+ SpatialCSGSetOperatorComplementsMustReferenceChildren, 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 2019-12-20 22:39:27 UTC (rev 26255)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-12-20 23:13:22 UTC (rev 26256)
@@ -295,8 +295,6 @@
, SpatialCSGSetOperatorAllowedAttributes = 1223203
, SpatialCSGSetOperatorAllowedElements = 1223204
, SpatialCSGSetOperatorOperationTypeMustBeSetOperationEnum = 1223205
-, SpatialCSGSetOperatorComplementAMustBeCSGNode = 1223206
-, SpatialCSGSetOperatorComplementBMustBeCSGNode = 1223207
, SpatialCSGSetOperatorLOCSGNodesAllowedCoreElements = 1223208
, SpatialCSGSetOperatorLOCSGNodesAllowedCoreAttributes = 1223209
, SpatialCSGSetOperatorTwoComplementsForDifference = 1223250
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-12-20 22:39:27 UTC (rev 26255)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-12-20 23:13:22 UTC (rev 26256)
@@ -2745,30 +2745,6 @@
}
},
- // 1223206
- { SpatialCSGSetOperatorComplementAMustBeCSGNode,
- "The attribute 'complementA' must point to CSGNode object.",
- LIBSBML_CAT_GENERAL_CONSISTENCY,
- LIBSBML_SEV_ERROR,
- "The value of the attribute 'spatial:complementA' of a <csgSetOperator> "
- "object must be the identifier of an existing <csgNode> object defined in "
- "the enclosing <model> object.",
- { "L3V1 Spatial V1 Section"
- }
- },
-
- // 1223207
- { SpatialCSGSetOperatorComplementBMustBeCSGNode,
- "The attribute 'complementB' must point to CSGNode object.",
- LIBSBML_CAT_GENERAL_CONSISTENCY,
- LIBSBML_SEV_ERROR,
- "The value of the attribute 'spatial:complementB' of a <csgSetOperator> "
- "object must be the identifier of an existing <csgNode> object defined in "
- "the enclosing <model> object.",
- { "L3V1 Spatial V1 Section"
- }
- },
-
// 1223208
{ SpatialCSGSetOperatorLOCSGNodesAllowedCoreElements,
"Core elements allowed on <listOfCSGNodes>.",
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-04.xml 2019-12-20 23:13:22 UTC (rev 26256)
@@ -0,0 +1,51 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="union">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere2" spatial:primitiveType="sphere"/>
+ <spatial:csgSetOperator spatial:operationType="difference" spatial:complementA="domainType_1" spatial:complementB="cube1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-05.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-05.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-05.xml 2019-12-20 23:13:22 UTC (rev 26256)
@@ -0,0 +1,51 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="union">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere2" spatial:primitiveType="sphere"/>
+ <spatial:csgSetOperator spatial:operationType="difference" spatial:complementA="sphere2" spatial:complementB="cube1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-06.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-06.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-06.xml 2019-12-20 23:13:22 UTC (rev 26256)
@@ -0,0 +1,51 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="union">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere2" spatial:primitiveType="sphere"/>
+ <spatial:csgSetOperator spatial:operationType="difference" spatial:complementA="some_circle" spatial:complementB="cube1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-pass-00-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-pass-00-02.xml 2019-12-20 23:13:22 UTC (rev 26256)
@@ -0,0 +1,51 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="union">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere2" spatial:primitiveType="sphere"/>
+ <spatial:csgSetOperator spatial:operationType="difference" spatial:complementA="sphere1" spatial:complementB="cube1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2019-12-20 22:39:28
|
Revision: 26255
http://sourceforge.net/p/sbml/code/26255
Author: luciansmith
Date: 2019-12-20 22:39:27 +0000 (Fri, 20 Dec 2019)
Log Message:
-----------
Add tests for spatial validation rule 23205.
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-pass-00-01.xml
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-fail-01-01.xml 2019-12-20 22:39:27 UTC (rev 26255)
@@ -0,0 +1,46 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="sameness" spatial:complementA="sphere1" spatial:complementB="cube1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-fail-01-02.xml 2019-12-20 22:39:27 UTC (rev 26255)
@@ -0,0 +1,46 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="conjunction" spatial:complementA="sphere1" spatial:complementB="cube1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-fail-01-03.xml 2019-12-20 22:39:27 UTC (rev 26255)
@@ -0,0 +1,46 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="conjunction junction; what's your function?" spatial:complementA="sphere1" spatial:complementB="cube1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223205-pass-00-01.xml 2019-12-20 22:39:27 UTC (rev 26255)
@@ -0,0 +1,46 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="difference" spatial:complementA="sphere1" spatial:complementB="cube1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2019-12-20 22:35:57
|
Revision: 26254
http://sourceforge.net/p/sbml/code/26254
Author: luciansmith
Date: 2019-12-20 22:35:56 +0000 (Fri, 20 Dec 2019)
Log Message:
-----------
Add tests for spatial validation rule 23104.
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-05.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-05.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-06.xml
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-01.xml 2019-12-20 22:35:56 UTC (rev 26254)
@@ -0,0 +1,41 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="triangle"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-02.xml 2019-12-20 22:35:56 UTC (rev 26254)
@@ -0,0 +1,41 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="cylendar"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-03.xml 2019-12-20 22:35:56 UTC (rev 26254)
@@ -0,0 +1,41 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="point"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-04.xml 2019-12-20 22:35:56 UTC (rev 26254)
@@ -0,0 +1,41 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="dodecahedron"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-05.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-05.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-fail-01-05.xml 2019-12-20 22:35:56 UTC (rev 26254)
@@ -0,0 +1,41 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="rightTriangle"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-01.xml 2019-12-20 22:35:56 UTC (rev 26254)
@@ -0,0 +1,41 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-02.xml 2019-12-20 22:35:56 UTC (rev 26254)
@@ -0,0 +1,41 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="x1" spatial:primitiveType="cube"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-03.xml 2019-12-20 22:35:56 UTC (rev 26254)
@@ -0,0 +1,41 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="x1" spatial:primitiveType="circle"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-04.xml 2019-12-20 22:35:56 UTC (rev 26254)
@@ -0,0 +1,41 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="x1" spatial:primitiveType="square"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-05.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-05.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-05.xml 2019-12-20 22:35:56 UTC (rev 26254)
@@ -0,0 +1,41 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="x1" spatial:primitiveType="cylinder"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-06.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-06.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223104-pass-00-06.xml 2019-12-20 22:35:56 UTC (rev 26254)
@@ -0,0 +1,41 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="x1" spatial:primitiveType="cone"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2019-12-20 22:15:36
|
Revision: 26253
http://sourceforge.net/p/sbml/code/26253
Author: luciansmith
Date: 2019-12-20 22:15:35 +0000 (Fri, 20 Dec 2019)
Log Message:
-----------
Fix capitalization of <csg*> elements in messages.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGNode.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGObject.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGPrimitive.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGRotation.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGScale.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGSetOperator.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGTranslation.cpp
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGNode.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGNode.cpp 2019-12-20 22:12:30 UTC (rev 26252)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGNode.cpp 2019-12-20 22:15:35 UTC (rev 26253)
@@ -750,7 +750,7 @@
{
if (mId.empty() == true)
{
- logEmptyString(mId, level, version, "<CSGNode>");
+ logEmptyString(mId, level, version, "<csgNode>");
}
else if (SyntaxChecker::isValidSBMLSId(mId) == false)
{
@@ -770,7 +770,7 @@
{
if (mName.empty() == true)
{
- logEmptyString(mName, level, version, "<CSGNode>");
+ logEmptyString(mName, level, version, "<csgNode>");
}
}
}
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGObject.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGObject.cpp 2019-12-20 22:12:30 UTC (rev 26252)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGObject.cpp 2019-12-20 22:15:35 UTC (rev 26253)
@@ -1553,7 +1553,7 @@
{
if (mId.empty() == true)
{
- logEmptyString(mId, level, version, "<CSGObject>");
+ logEmptyString(mId, level, version, "<csgObject>");
}
else if (SyntaxChecker::isValidSBMLSId(mId) == false)
{
@@ -1565,7 +1565,7 @@
else
{
std::string message = "Spatial attribute 'id' is missing from the "
- "<CSGObject> element.";
+ "<csgObject> element.";
log->logPackageError("spatial", SpatialCSGObjectAllowedAttributes,
pkgVersion, level, version, message, getLine(), getColumn());
}
@@ -1580,7 +1580,7 @@
{
if (mName.empty() == true)
{
- logEmptyString(mName, level, version, "<CSGObject>");
+ logEmptyString(mName, level, version, "<csgObject>");
}
}
@@ -1594,7 +1594,7 @@
{
if (mDomainType.empty() == true)
{
- logEmptyString(mDomainType, level, version, "<CSGObject>");
+ logEmptyString(mDomainType, level, version, "<csgObject>");
}
else if (SyntaxChecker::isValidSBMLSId(mDomainType) == false)
{
@@ -1615,7 +1615,7 @@
else
{
std::string message = "Spatial attribute 'domainType' is missing from the "
- "<CSGObject> element.";
+ "<csgObject> element.";
log->logPackageError("spatial", SpatialCSGObjectAllowedAttributes,
pkgVersion, level, version, message, getLine(), getColumn());
}
@@ -1633,7 +1633,7 @@
log->contains(XMLAttributeTypeMismatch))
{
log->remove(XMLAttributeTypeMismatch);
- std::string message = "Spatial attribute 'ordinal' from the <CSGObject> "
+ std::string message = "Spatial attribute 'ordinal' from the <csgObject> "
"element must be an integer.";
log->logPackageError("spatial", SpatialCSGObjectOrdinalMustBeInteger,
pkgVersion, level, version, message, getLine(), getColumn());
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGPrimitive.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGPrimitive.cpp 2019-12-20 22:12:30 UTC (rev 26252)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGPrimitive.cpp 2019-12-20 22:15:35 UTC (rev 26253)
@@ -631,7 +631,7 @@
{
if (primitiveType.empty() == true)
{
- logEmptyString(primitiveType, level, version, "<CSGPrimitive>");
+ logEmptyString(primitiveType, level, version, "<csgPrimitive>");
}
else
{
@@ -639,7 +639,7 @@
if (PrimitiveKind_isValid(mPrimitiveType) == 0)
{
- std::string msg = "The primitiveType on the <CSGPrimitive> ";
+ std::string msg = "The primitiveType on the <csgPrimitive> ";
if (isSetId())
{
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGRotation.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGRotation.cpp 2019-12-20 22:12:30 UTC (rev 26252)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGRotation.cpp 2019-12-20 22:15:35 UTC (rev 26253)
@@ -856,7 +856,7 @@
log->contains(XMLAttributeTypeMismatch))
{
log->remove(XMLAttributeTypeMismatch);
- std::string message = "Spatial attribute 'rotateX' from the <CSGRotation> "
+ std::string message = "Spatial attribute 'rotateX' from the <csgRotation> "
"element must be an integer.";
log->logPackageError("spatial", SpatialCSGRotationRotateXMustBeDouble,
pkgVersion, level, version, message, getLine(), getColumn());
@@ -864,7 +864,7 @@
else
{
std::string message = "Spatial attribute 'rotateX' is missing from the "
- "<CSGRotation> element.";
+ "<csgRotation> element.";
log->logPackageError("spatial", SpatialCSGRotationAllowedAttributes,
pkgVersion, level, version, message, getLine(), getColumn());
}
@@ -883,7 +883,7 @@
log->contains(XMLAttributeTypeMismatch))
{
log->remove(XMLAttributeTypeMismatch);
- std::string message = "Spatial attribute 'rotateY' from the <CSGRotation> "
+ std::string message = "Spatial attribute 'rotateY' from the <csgRotation> "
"element must be an integer.";
log->logPackageError("spatial", SpatialCSGRotationRotateYMustBeDouble,
pkgVersion, level, version, message, getLine(), getColumn());
@@ -903,7 +903,7 @@
log->contains(XMLAttributeTypeMismatch))
{
log->remove(XMLAttributeTypeMismatch);
- std::string message = "Spatial attribute 'rotateZ' from the <CSGRotation> "
+ std::string message = "Spatial attribute 'rotateZ' from the <csgRotation> "
"element must be an integer.";
log->logPackageError("spatial", SpatialCSGRotationRotateZMustBeDouble,
pkgVersion, level, version, message, getLine(), getColumn());
@@ -925,7 +925,7 @@
{
log->remove(XMLAttributeTypeMismatch);
std::string message = "Spatial attribute 'rotateAngleInRadians' from the "
- "<CSGRotation> element must be an integer.";
+ "<csgRotation> element must be an integer.";
log->logPackageError("spatial",
SpatialCSGRotationRotateAngleInRadiansMustBeDouble, pkgVersion, level,
version, message, getLine(), getColumn());
@@ -933,7 +933,7 @@
else
{
std::string message = "Spatial attribute 'rotateAngleInRadians' is "
- "missing from the <CSGRotation> element.";
+ "missing from the <csgRotation> element.";
log->logPackageError("spatial", SpatialCSGRotationAllowedAttributes,
pkgVersion, level, version, message, getLine(), getColumn());
}
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGScale.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGScale.cpp 2019-12-20 22:12:30 UTC (rev 26252)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGScale.cpp 2019-12-20 22:15:35 UTC (rev 26253)
@@ -763,7 +763,7 @@
log->contains(XMLAttributeTypeMismatch))
{
log->remove(XMLAttributeTypeMismatch);
- std::string message = "Spatial attribute 'scaleX' from the <CSGScale> "
+ std::string message = "Spatial attribute 'scaleX' from the <csgScale> "
"element must be an integer.";
log->logPackageError("spatial", SpatialCSGScaleScaleXMustBeDouble,
pkgVersion, level, version, message, getLine(), getColumn());
@@ -771,7 +771,7 @@
else
{
std::string message = "Spatial attribute 'scaleX' is missing from the "
- "<CSGScale> element.";
+ "<csgScale> element.";
log->logPackageError("spatial", SpatialCSGScaleAllowedAttributes,
pkgVersion, level, version, message, getLine(), getColumn());
}
@@ -790,7 +790,7 @@
log->contains(XMLAttributeTypeMismatch))
{
log->remove(XMLAttributeTypeMismatch);
- std::string message = "Spatial attribute 'scaleY' from the <CSGScale> "
+ std::string message = "Spatial attribute 'scaleY' from the <csgScale> "
"element must be an integer.";
log->logPackageError("spatial", SpatialCSGScaleScaleYMustBeDouble,
pkgVersion, level, version, message, getLine(), getColumn());
@@ -810,7 +810,7 @@
log->contains(XMLAttributeTypeMismatch))
{
log->remove(XMLAttributeTypeMismatch);
- std::string message = "Spatial attribute 'scaleZ' from the <CSGScale> "
+ std::string message = "Spatial attribute 'scaleZ' from the <csgScale> "
"element must be an integer.";
log->logPackageError("spatial", SpatialCSGScaleScaleZMustBeDouble,
pkgVersion, level, version, message, getLine(), getColumn());
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGSetOperator.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGSetOperator.cpp 2019-12-20 22:12:30 UTC (rev 26252)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGSetOperator.cpp 2019-12-20 22:15:35 UTC (rev 26253)
@@ -1452,7 +1452,7 @@
{
if (operationType.empty() == true)
{
- logEmptyString(operationType, level, version, "<CSGSetOperator>");
+ logEmptyString(operationType, level, version, "<csgSetOperator>");
}
else
{
@@ -1460,7 +1460,7 @@
if (SetOperation_isValid(mOperationType) == 0)
{
- std::string msg = "The operationType on the <CSGSetOperator> ";
+ std::string msg = "The operationType on the <csgSetOperator> ";
if (isSetId())
{
@@ -1492,7 +1492,7 @@
{
if (mComplementA.empty() == true)
{
- logEmptyString(mComplementA, level, version, "<CSGSetOperator>");
+ logEmptyString(mComplementA, level, version, "<csgSetOperator>");
}
else if (SyntaxChecker::isValidSBMLSId(mComplementA) == false)
{
@@ -1521,7 +1521,7 @@
{
if (mComplementB.empty() == true)
{
- logEmptyString(mComplementB, level, version, "<CSGSetOperator>");
+ logEmptyString(mComplementB, level, version, "<csgSetOperator>");
}
else if (SyntaxChecker::isValidSBMLSId(mComplementB) == false)
{
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGTranslation.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGTranslation.cpp 2019-12-20 22:12:30 UTC (rev 26252)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGTranslation.cpp 2019-12-20 22:15:35 UTC (rev 26253)
@@ -772,7 +772,7 @@
{
log->remove(XMLAttributeTypeMismatch);
std::string message = "Spatial attribute 'translateX' from the "
- "<CSGTranslation> element must be an integer.";
+ "<csgTranslation> element must be an integer.";
log->logPackageError("spatial",
SpatialCSGTranslationTranslateXMustBeDouble, pkgVersion, level, version,
message, getLine(), getColumn());
@@ -780,7 +780,7 @@
else
{
std::string message = "Spatial attribute 'translateX' is missing from the "
- "<CSGTranslation> element.";
+ "<csgTranslation> element.";
log->logPackageError("spatial", SpatialCSGTranslationAllowedAttributes,
pkgVersion, level, version, message, getLine(), getColumn());
}
@@ -800,7 +800,7 @@
{
log->remove(XMLAttributeTypeMismatch);
std::string message = "Spatial attribute 'translateY' from the "
- "<CSGTranslation> element must be an integer.";
+ "<csgTranslation> element must be an integer.";
log->logPackageError("spatial",
SpatialCSGTranslationTranslateYMustBeDouble, pkgVersion, level, version,
message, getLine(), getColumn());
@@ -821,7 +821,7 @@
{
log->remove(XMLAttributeTypeMismatch);
std::string message = "Spatial attribute 'translateZ' from the "
- "<CSGTranslation> element must be an integer.";
+ "<csgTranslation> element must be an integer.";
log->logPackageError("spatial",
SpatialCSGTranslationTranslateZMustBeDouble, pkgVersion, level, version,
message, getLine(), getColumn());
|
|
From: <luc...@us...> - 2019-12-20 22:12:32
|
Revision: 26252
http://sourceforge.net/p/sbml/code/26252
Author: luciansmith
Date: 2019-12-20 22:12:30 +0000 (Fri, 20 Dec 2019)
Log Message:
-----------
Add tests for spatial validation rule 222804-6.
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222804-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222804-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222805-fail-01-01-1222851.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222805-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222806-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222806-pass-00-01.xml
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222804-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222804-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222804-fail-01-01.xml 2019-12-20 22:12:30 UTC (rev 26252)
@@ -0,0 +1,43 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgScale spatial:scaleX="vewy vewy small" spatial:scaleY="0.3" spatial:scaleZ="0.4">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ </spatial:csgScale>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222804-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222804-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222804-pass-00-01.xml 2019-12-20 22:12:30 UTC (rev 26252)
@@ -0,0 +1,43 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgScale spatial:scaleX="0.2" spatial:scaleY="0.3" spatial:scaleZ="0.4">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ </spatial:csgScale>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222805-fail-01-01-1222851.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222805-fail-01-01-1222851.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222805-fail-01-01-1222851.xml 2019-12-20 22:12:30 UTC (rev 26252)
@@ -0,0 +1,43 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgScale spatial:scaleX="0.2" spatial:scaleY="whatever, dude" spatial:scaleZ="0.4">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ </spatial:csgScale>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222805-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222805-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222805-pass-00-01.xml 2019-12-20 22:12:30 UTC (rev 26252)
@@ -0,0 +1,43 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgScale spatial:scaleX="0.2" spatial:scaleY="0.3" spatial:scaleZ="0.4">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ </spatial:csgScale>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222806-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222806-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222806-fail-01-01.xml 2019-12-20 22:12:30 UTC (rev 26252)
@@ -0,0 +1,39 @@
+<?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_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:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="2"/>
+ </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:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgScale spatial:scaleX="0.2" spatial:scaleY="0.3" spatial:scaleZ="I will die on this hill! I will never surrender!">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ </spatial:csgScale>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222806-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222806-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222806-pass-00-01.xml 2019-12-20 22:12:30 UTC (rev 26252)
@@ -0,0 +1,43 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgScale spatial:scaleX="0.2" spatial:scaleY="0.3" spatial:scaleZ="0.4">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ </spatial:csgScale>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2019-12-20 22:07:56
|
Revision: 26251
http://sourceforge.net/p/sbml/code/26251
Author: luciansmith
Date: 2019-12-20 22:07:54 +0000 (Fri, 20 Dec 2019)
Log Message:
-----------
Add tests for spatial validation rule 223704-7.
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222704-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222704-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222705-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222705-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222706-fail-01-01-1222751.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222706-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222707-false-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222707-pass-00-01.xml
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222704-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222704-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222704-fail-01-01.xml 2019-12-20 22:07:54 UTC (rev 26251)
@@ -0,0 +1,43 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgRotation spatial:rotateX="point2" spatial:rotateY="0.3" spatial:rotateZ="0.4" spatial:rotateAngleInRadians="2.7">
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:csgRotation>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222704-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222704-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222704-pass-00-01.xml 2019-12-20 22:07:54 UTC (rev 26251)
@@ -0,0 +1,43 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgRotation spatial:rotateX="0.2" spatial:rotateY="0.3" spatial:rotateZ="0.4" spatial:rotateAngleInRadians="2.7">
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:csgRotation>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222705-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222705-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222705-fail-01-01.xml 2019-12-20 22:07:54 UTC (rev 26251)
@@ -0,0 +1,43 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgRotation spatial:rotateX="0.2" spatial:rotateY="0.3" spatial:rotateZ="0.4" spatial:rotateAngleInRadians="at_least_twenty_seven">
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:csgRotation>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222705-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222705-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222705-pass-00-01.xml 2019-12-20 22:07:54 UTC (rev 26251)
@@ -0,0 +1,43 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgRotation spatial:rotateX="0.2" spatial:rotateY="0.3" spatial:rotateZ="0.4" spatial:rotateAngleInRadians="2.7">
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:csgRotation>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222706-fail-01-01-1222751.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222706-fail-01-01-1222751.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222706-fail-01-01-1222751.xml 2019-12-20 22:07:54 UTC (rev 26251)
@@ -0,0 +1,43 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgRotation spatial:rotateX="0.2" spatial:rotateY="none" spatial:rotateZ="0.4" spatial:rotateAngleInRadians="2.7">
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:csgRotation>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222706-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222706-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222706-pass-00-01.xml 2019-12-20 22:07:54 UTC (rev 26251)
@@ -0,0 +1,43 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgRotation spatial:rotateX="0.2" spatial:rotateY="0.3" spatial:rotateZ="0.4" spatial:rotateAngleInRadians="2.7">
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:csgRotation>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222707-false-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222707-false-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222707-false-01-01.xml 2019-12-20 22:07:54 UTC (rev 26251)
@@ -0,0 +1,39 @@
+<?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_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:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="2"/>
+ </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:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgRotation spatial:rotateX="0.2" spatial:rotateY="0.3" spatial:rotateZ="false" spatial:rotateAngleInRadians="2.7">
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:csgRotation>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222707-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222707-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222707-pass-00-01.xml 2019-12-20 22:07:54 UTC (rev 26251)
@@ -0,0 +1,43 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgRotation spatial:rotateX="0.2" spatial:rotateY="0.3" spatial:rotateZ="0.4" spatial:rotateAngleInRadians="2.7">
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:csgRotation>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2019-12-20 21:59:38
|
Revision: 26250
http://sourceforge.net/p/sbml/code/26250
Author: luciansmith
Date: 2019-12-20 21:59:36 +0000 (Fri, 20 Dec 2019)
Log Message:
-----------
Add tests for spatial validation rule 223604-6.
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222604-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222604-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222605-fail-01-01-1222651.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222605-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222606-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222606-pass-00-01.xml
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222604-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222604-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222604-fail-01-01.xml 2019-12-20 21:59:36 UTC (rev 26250)
@@ -0,0 +1,43 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgTranslation spatial:translateX="pointTwo" spatial:translateY="0.3" spatial:translateZ="0.4">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ </spatial:csgTranslation>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222604-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222604-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222604-pass-00-01.xml 2019-12-20 21:59:36 UTC (rev 26250)
@@ -0,0 +1,43 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgTranslation spatial:translateX="0.2" spatial:translateY="0.3" spatial:translateZ="0.4">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ </spatial:csgTranslation>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222605-fail-01-01-1222651.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222605-fail-01-01-1222651.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222605-fail-01-01-1222651.xml 2019-12-20 21:59:36 UTC (rev 26250)
@@ -0,0 +1,43 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgTranslation spatial:translateX="0.2" spatial:translateY="negative twenty" spatial:translateZ="0.4">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ </spatial:csgTranslation>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222605-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222605-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222605-pass-00-01.xml 2019-12-20 21:59:36 UTC (rev 26250)
@@ -0,0 +1,43 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgTranslation spatial:translateX="0.2" spatial:translateY="0.3" spatial:translateZ="0.4">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ </spatial:csgTranslation>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222606-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222606-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222606-fail-01-01.xml 2019-12-20 21:59:36 UTC (rev 26250)
@@ -0,0 +1,39 @@
+<?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_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:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="2"/>
+ </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:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgTranslation spatial:translateX="0.2" spatial:translateY="0.3" spatial:translateZ="infinity and beyond">
+ <spatial:csgPrimitive spatial:id="circle1" spatial:primitiveType="circle"/>
+ </spatial:csgTranslation>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222606-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222606-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222606-pass-00-01.xml 2019-12-20 21:59:36 UTC (rev 26250)
@@ -0,0 +1,43 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgTranslation spatial:translateX="0.2" spatial:translateY="0.3" spatial:translateZ="0.4">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ </spatial:csgTranslation>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2019-12-20 21:53:06
|
Revision: 26249
http://sourceforge.net/p/sbml/code/26249
Author: luciansmith
Date: 2019-12-20 21:53:04 +0000 (Fri, 20 Dec 2019)
Log Message:
-----------
Add tests for spatial validation rule 22307.
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222307-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222307-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222307-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222307-pass-00-01.xml
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222307-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222307-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222307-fail-01-01.xml 2019-12-20 21:53:04 UTC (rev 26249)
@@ -0,0 +1,41 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="one">
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222307-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222307-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222307-fail-01-02.xml 2019-12-20 21:53:04 UTC (rev 26249)
@@ -0,0 +1,41 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="1+">
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222307-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222307-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222307-fail-01-03.xml 2019-12-20 21:53:04 UTC (rev 26249)
@@ -0,0 +1,41 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="1.0002">
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222307-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222307-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222307-pass-00-01.xml 2019-12-20 21:53:04 UTC (rev 26249)
@@ -0,0 +1,41 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="1">
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2019-12-20 21:16:55
|
Revision: 26248
http://sourceforge.net/p/sbml/code/26248
Author: luciansmith
Date: 2019-12-20 21:16:53 +0000 (Fri, 20 Dec 2019)
Log Message:
-----------
Add tests for spatial validation rules 22104, 7, 8, and 10.
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222104-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222104-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222104-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222107-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222107-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222107-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222108-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222108-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222108-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222108-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-pass-00-01.xml
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222104-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222104-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222104-fail-01-01.xml 2019-12-20 21:16:53 UTC (rev 26248)
@@ -0,0 +1,40 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:parametricGeometry spatial:id="geometryDefinition_3" spatial:isActive="true">
+ <spatial:spatialPoints spatial:arrayDataLength="9" spatial:compression="uncompressed" spatial:dataType="double" spatial:id="spatialPoints_1">0 0 0, 0 1 0, 0 1 1</spatial:spatialPoints>
+ <spatial:listOfParametricObjects>
+ <spatial:parametricObject spatial:compression="uncompressed" spatial:dataType="double" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:pointIndexLength="3" spatial:polygonType="circle">0 1 2</spatial:parametricObject>
+ </spatial:listOfParametricObjects>
+ </spatial:parametricGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222104-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222104-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222104-fail-01-02.xml 2019-12-20 21:16:53 UTC (rev 26248)
@@ -0,0 +1,40 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:parametricGeometry spatial:id="geometryDefinition_3" spatial:isActive="true">
+ <spatial:spatialPoints spatial:arrayDataLength="9" spatial:compression="uncompressed" spatial:dataType="double" spatial:id="spatialPoints_1">0 0 0, 0 1 0, 0 1 1</spatial:spatialPoints>
+ <spatial:listOfParametricObjects>
+ <spatial:parametricObject spatial:compression="uncompressed" spatial:dataType="double" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:pointIndexLength="3" spatial:polygonType="pentagon">0 1 2</spatial:parametricObject>
+ </spatial:listOfParametricObjects>
+ </spatial:parametricGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222104-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222104-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222104-pass-00-01.xml 2019-12-20 21:16:53 UTC (rev 26248)
@@ -0,0 +1,40 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:parametricGeometry spatial:id="geometryDefinition_3" spatial:isActive="true">
+ <spatial:spatialPoints spatial:arrayDataLength="9" spatial:compression="uncompressed" spatial:dataType="double" spatial:id="spatialPoints_1">0 0 0, 0 1 0, 0 1 1</spatial:spatialPoints>
+ <spatial:listOfParametricObjects>
+ <spatial:parametricObject spatial:compression="uncompressed" spatial:dataType="double" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:pointIndexLength="3" spatial:polygonType="triangle">0 1 2</spatial:parametricObject>
+ </spatial:listOfParametricObjects>
+ </spatial:parametricGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222107-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222107-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222107-fail-01-01.xml 2019-12-20 21:16:53 UTC (rev 26248)
@@ -0,0 +1,40 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:parametricGeometry spatial:id="geometryDefinition_3" spatial:isActive="true">
+ <spatial:spatialPoints spatial:arrayDataLength="9" spatial:compression="uncompressed" spatial:dataType="double" spatial:id="spatialPoints_1">0 0 0, 0 1 0, 0 1 1</spatial:spatialPoints>
+ <spatial:listOfParametricObjects>
+ <spatial:parametricObject spatial:compression="uncompressed" spatial:dataType="double" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:pointIndexLength="three" spatial:polygonType="triangle">0 1 2</spatial:parametricObject>
+ </spatial:listOfParametricObjects>
+ </spatial:parametricGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222107-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222107-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222107-fail-01-02.xml 2019-12-20 21:16:53 UTC (rev 26248)
@@ -0,0 +1,40 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:parametricGeometry spatial:id="geometryDefinition_3" spatial:isActive="true">
+ <spatial:spatialPoints spatial:arrayDataLength="9" spatial:compression="uncompressed" spatial:dataType="double" spatial:id="spatialPoints_1">0 0 0, 0 1 0, 0 1 1</spatial:spatialPoints>
+ <spatial:listOfParametricObjects>
+ <spatial:parametricObject spatial:compression="uncompressed" spatial:dataType="double" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:pointIndexLength="3.4" spatial:polygonType="triangle">0 1 2</spatial:parametricObject>
+ </spatial:listOfParametricObjects>
+ </spatial:parametricGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222107-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222107-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222107-pass-00-01.xml 2019-12-20 21:16:53 UTC (rev 26248)
@@ -0,0 +1,40 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:parametricGeometry spatial:id="geometryDefinition_3" spatial:isActive="true">
+ <spatial:spatialPoints spatial:arrayDataLength="9" spatial:compression="uncompressed" spatial:dataType="double" spatial:id="spatialPoints_1">0 0 0, 0 1 0, 0 1 1</spatial:spatialPoints>
+ <spatial:listOfParametricObjects>
+ <spatial:parametricObject spatial:compression="uncompressed" spatial:dataType="double" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:pointIndexLength="3" spatial:polygonType="triangle">0 1 2</spatial:parametricObject>
+ </spatial:listOfParametricObjects>
+ </spatial:parametricGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222108-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222108-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222108-fail-01-01.xml 2019-12-20 21:16:53 UTC (rev 26248)
@@ -0,0 +1,40 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:parametricGeometry spatial:id="geometryDefinition_3" spatial:isActive="true">
+ <spatial:spatialPoints spatial:arrayDataLength="9" spatial:compression="uncompressed" spatial:dataType="double" spatial:id="spatialPoints_1">0 0 0, 0 1 0, 0 1 1</spatial:spatialPoints>
+ <spatial:listOfParametricObjects>
+ <spatial:parametricObject spatial:compression="compressed" spatial:dataType="double" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:pointIndexLength="3" spatial:polygonType="triangle">0 1 2</spatial:parametricObject>
+ </spatial:listOfParametricObjects>
+ </spatial:parametricGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222108-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222108-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222108-fail-01-02.xml 2019-12-20 21:16:53 UTC (rev 26248)
@@ -0,0 +1,40 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:parametricGeometry spatial:id="geometryDefinition_3" spatial:isActive="true">
+ <spatial:spatialPoints spatial:arrayDataLength="9" spatial:compression="uncompressed" spatial:dataType="double" spatial:id="spatialPoints_1">0 0 0, 0 1 0, 0 1 1</spatial:spatialPoints>
+ <spatial:listOfParametricObjects>
+ <spatial:parametricObject spatial:compression="not compressed" spatial:dataType="double" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:pointIndexLength="3" spatial:polygonType="triangle">0 1 2</spatial:parametricObject>
+ </spatial:listOfParametricObjects>
+ </spatial:parametricGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222108-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222108-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222108-fail-01-03.xml 2019-12-20 21:16:53 UTC (rev 26248)
@@ -0,0 +1,40 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:parametricGeometry spatial:id="geometryDefinition_3" spatial:isActive="true">
+ <spatial:spatialPoints spatial:arrayDataLength="9" spatial:compression="uncompressed" spatial:dataType="double" spatial:id="spatialPoints_1">0 0 0, 0 1 0, 0 1 1</spatial:spatialPoints>
+ <spatial:listOfParametricObjects>
+ <spatial:parametricObject spatial:compression="0" spatial:dataType="double" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:pointIndexLength="3" spatial:polygonType="triangle">0 1 2</spatial:parametricObject>
+ </spatial:listOfParametricObjects>
+ </spatial:parametricGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222108-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222108-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222108-pass-00-01.xml 2019-12-20 21:16:53 UTC (rev 26248)
@@ -0,0 +1,40 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:parametricGeometry spatial:id="geometryDefinition_3" spatial:isActive="true">
+ <spatial:spatialPoints spatial:arrayDataLength="9" spatial:compression="uncompressed" spatial:dataType="double" spatial:id="spatialPoints_1">0 0 0, 0 1 0, 0 1 1</spatial:spatialPoints>
+ <spatial:listOfParametricObjects>
+ <spatial:parametricObject spatial:compression="uncompressed" spatial:dataType="double" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:pointIndexLength="3" spatial:polygonType="triangle">0 1 2</spatial:parametricObject>
+ </spatial:listOfParametricObjects>
+ </spatial:parametricGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-fail-01-01.xml 2019-12-20 21:16:53 UTC (rev 26248)
@@ -0,0 +1,40 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:parametricGeometry spatial:id="geometryDefinition_3" spatial:isActive="true">
+ <spatial:spatialPoints spatial:arrayDataLength="9" spatial:compression="uncompressed" spatial:dataType="double" spatial:id="spatialPoints_1">0 0 0, 0 1 0, 0 1 1</spatial:spatialPoints>
+ <spatial:listOfParametricObjects>
+ <spatial:parametricObject spatial:compression="uncompressed" spatial:dataType="2xfloat" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:pointIndexLength="3" spatial:polygonType="triangle">0 1 2</spatial:parametricObject>
+ </spatial:listOfParametricObjects>
+ </spatial:parametricGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-fail-01-02.xml 2019-12-20 21:16:53 UTC (rev 26248)
@@ -0,0 +1,40 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:parametricGeometry spatial:id="geometryDefinition_3" spatial:isActive="true">
+ <spatial:spatialPoints spatial:arrayDataLength="9" spatial:compression="uncompressed" spatial:dataType="double" spatial:id="spatialPoints_1">0 0 0, 0 1 0, 0 1 1</spatial:spatialPoints>
+ <spatial:listOfParametricObjects>
+ <spatial:parametricObject spatial:compression="uncompressed" spatial:dataType="string" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:pointIndexLength="3" spatial:polygonType="triangle">0 1 2</spatial:parametricObject>
+ </spatial:listOfParametricObjects>
+ </spatial:parametricGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-fail-01-03.xml 2019-12-20 21:16:53 UTC (rev 26248)
@@ -0,0 +1,40 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:parametricGeometry spatial:id="geometryDefinition_3" spatial:isActive="true">
+ <spatial:spatialPoints spatial:arrayDataLength="9" spatial:compression="uncompressed" spatial:dataType="double" spatial:id="spatialPoints_1">0 0 0, 0 1 0, 0 1 1</spatial:spatialPoints>
+ <spatial:listOfParametricObjects>
+ <spatial:parametricObject spatial:compression="uncompressed" spatial:dataType="bool" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:pointIndexLength="3" spatial:polygonType="triangle">0 1 2</spatial:parametricObject>
+ </spatial:listOfParametricObjects>
+ </spatial:parametricGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-fail-01-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-fail-01-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-fail-01-04.xml 2019-12-20 21:16:53 UTC (rev 26248)
@@ -0,0 +1,40 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:parametricGeometry spatial:id="geometryDefinition_3" spatial:isActive="true">
+ <spatial:spatialPoints spatial:arrayDataLength="9" spatial:compression="uncompressed" spatial:dataType="double" spatial:id="spatialPoints_1">0 0 0, 0 1 0, 0 1 1</spatial:spatialPoints>
+ <spatial:listOfParametricObjects>
+ <spatial:parametricObject spatial:compression="uncompressed" spatial:dataType="true" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:pointIndexLength="3" spatial:polygonType="triangle">0 1 2</spatial:parametricObject>
+ </spatial:listOfParametricObjects>
+ </spatial:parametricGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222110-pass-00-01.xml 2019-12-20 21:16:53 UTC (rev 26248)
@@ -0,0 +1,40 @@
+<?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_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_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>
+ </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:listOfGeometryDefinitions>
+ <spatial:parametricGeometry spatial:id="geometryDefinition_3" spatial:isActive="true">
+ <spatial:spatialPoints spatial:arrayDataLength="9" spatial:compression="uncompressed" spatial:dataType="double" spatial:id="spatialPoints_1">0 0 0, 0 1 0, 0 1 1</spatial:spatialPoints>
+ <spatial:listOfParametricObjects>
+ <spatial:parametricObject spatial:compression="uncompressed" spatial:dataType="double" spatial:domainType="domainType_1" spatial:id="parametricObject_1" spatial:pointIndexLength="3" spatial:polygonType="triangle">0 1 2</spatial:parametricObject>
+ </spatial:listOfParametricObjects>
+ </spatial:parametricGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
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