You can subscribe to this list here.
2008 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
(121) |
Aug
(343) |
Sep
(98) |
Oct
(55) |
Nov
(158) |
Dec
(219) |
---|---|---|---|---|---|---|---|---|---|---|---|---|
2009 |
Jan
(278) |
Feb
(170) |
Mar
(286) |
Apr
(32) |
May
(83) |
Jun
(140) |
Jul
(212) |
Aug
(242) |
Sep
(52) |
Oct
(29) |
Nov
(132) |
Dec
(259) |
2010 |
Jan
(251) |
Feb
(147) |
Mar
(76) |
Apr
(140) |
May
(43) |
Jun
(66) |
Jul
(273) |
Aug
(205) |
Sep
(260) |
Oct
(100) |
Nov
(58) |
Dec
(264) |
2011 |
Jan
(219) |
Feb
(344) |
Mar
(320) |
Apr
(334) |
May
(125) |
Jun
(131) |
Jul
(195) |
Aug
(155) |
Sep
(55) |
Oct
(261) |
Nov
(286) |
Dec
(216) |
2012 |
Jan
(188) |
Feb
(177) |
Mar
(39) |
Apr
(179) |
May
(148) |
Jun
(43) |
Jul
(229) |
Aug
(104) |
Sep
(76) |
Oct
(82) |
Nov
(93) |
Dec
(180) |
2013 |
Jan
(323) |
Feb
(335) |
Mar
(35) |
Apr
(220) |
May
(238) |
Jun
(122) |
Jul
(316) |
Aug
(73) |
Sep
(135) |
Oct
(515) |
Nov
(320) |
Dec
(185) |
2014 |
Jan
(81) |
Feb
(146) |
Mar
(337) |
Apr
(234) |
May
(112) |
Jun
(239) |
Jul
(323) |
Aug
(123) |
Sep
(83) |
Oct
(285) |
Nov
(321) |
Dec
(96) |
2015 |
Jan
(77) |
Feb
(79) |
Mar
(124) |
Apr
(71) |
May
(35) |
Jun
(45) |
Jul
(77) |
Aug
(44) |
Sep
(22) |
Oct
(84) |
Nov
(120) |
Dec
(37) |
2016 |
Jan
(38) |
Feb
(74) |
Mar
(242) |
Apr
(153) |
May
(59) |
Jun
(44) |
Jul
(67) |
Aug
(74) |
Sep
(150) |
Oct
(35) |
Nov
(69) |
Dec
(43) |
2017 |
Jan
(43) |
Feb
(9) |
Mar
(274) |
Apr
(40) |
May
(81) |
Jun
(81) |
Jul
(87) |
Aug
(46) |
Sep
(98) |
Oct
(50) |
Nov
(220) |
Dec
(66) |
2018 |
Jan
(110) |
Feb
(22) |
Mar
(20) |
Apr
(147) |
May
(148) |
Jun
(30) |
Jul
(83) |
Aug
(63) |
Sep
(40) |
Oct
(53) |
Nov
(51) |
Dec
(104) |
2019 |
Jan
(14) |
Feb
(81) |
Mar
(80) |
Apr
(102) |
May
(16) |
Jun
(5) |
Jul
(34) |
Aug
(24) |
Sep
(9) |
Oct
(12) |
Nov
(42) |
Dec
(76) |
2020 |
Jan
(15) |
Feb
(11) |
Mar
(12) |
Apr
(7) |
May
(6) |
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
2021 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
(1) |
Nov
|
Dec
|
2022 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
(5) |
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
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 branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222105-fail-01-01.xml branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222105-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 branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222305-fail-01-01.xml branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222305-pass-00-01.xml 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 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 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 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 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 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 Property Changed: ---------------- 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 branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222105-fail-01-01.xml branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222105-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 branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222305-fail-01-01.xml branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1222305-pass-00-01.xml 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 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 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 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 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 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> + |