sbml-svn Mailing List for Systems Biology Markup Language (SBML) (Page 9)

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Revision: 26120
          http://sourceforge.net/p/sbml/code/26120
Author:   luciansmith
Date:     2019-08-29 23:04:36 +0000 (Thu, 29 Aug 2019)
Log Message:
-----------
Add validation rule spatial-21750.  Also fix its name.

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/1221750-fail-01-01.xml
    branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-pass-00-01.xml

Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
===================================================================

--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h	2019-08-29 22:51:56 UTC (rev 26119)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h	2019-08-29 23:04:36 UTC (rev 26120)
@@ -158,8 +158,8 @@
 , SpatialSampledVolumeSampledValueMustBeDouble                = 1221706
 , SpatialSampledVolumeMinValueMustBeDouble                    = 1221707
 , SpatialSampledVolumeMaxValueMustBeDouble                    = 1221708
-, SpatialSampledVolumeNeedsMinWithMax                         = 1221750
-, SpatialSampledVolumeNeedsMaxWithMin                         = 1221751
+, SpatialSampledVolumeNeedsMaxWithMin                         = 1221750
+, SpatialSampledVolumeNeedsMinWithMax                         = 1221751
 , SpatialSampledVolumeNoSampledValueWithMinMax                = 1221752
 , SpatialSampledVolumeNoMinMaxWithSampledValue                = 1221753
 , SpatialSampledVolumeMinMaxOrSampledValue                    = 1221754

Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h	2019-08-29 22:51:56 UTC (rev 26119)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h	2019-08-29 23:04:36 UTC (rev 26120)
@@ -1199,7 +1199,7 @@
   },
 
   // 1221750
-  { SpatialSampledVolumeNeedsMinWithMax,
+  { SpatialSampledVolumeNeedsMaxWithMin,
     "A 'minValue' attribute goes with the 'maxValue' attribute.",
     LIBSBML_CAT_GENERAL_CONSISTENCY,
     LIBSBML_SEV_ERROR,
@@ -1209,7 +1209,7 @@
   },
 
   // 1221751
-  { SpatialSampledVolumeNeedsMaxWithMin,
+  { SpatialSampledVolumeNeedsMinWithMax,
     "A 'maxValue' attribute goes with the 'minValue' attribute.",
     LIBSBML_CAT_GENERAL_CONSISTENCY,
     LIBSBML_SEV_ERROR,

Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp	2019-08-29 22:51:56 UTC (rev 26119)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp	2019-08-29 23:04:36 UTC (rev 26120)
@@ -523,5 +523,26 @@
 END_CONSTRAINT
 
 
+// 1221750
+START_CONSTRAINT(SpatialSampledVolumeNeedsMaxWithMin, SampledVolume, svol)
+{
+  bool fail = false;
+  if (svol.isSetMinValue() && !svol.isSetMaxValue()) {
+    fail = true;
+    stringstream ss_msg;
+    ss_msg << "A SampledVolume";
+    if (svol.isSetId())
+    {
+      ss_msg << " with id '" << svol.getId() << "'";
+    }
+    ss_msg << " has a minValue of '" << svol.getMinValue() << "', but does not set the maxValue attribute.";
+    msg = ss_msg.str();
+  }
+
+  inv(fail == false);
+}
+END_CONSTRAINT
+
+
 /** @endcond */
 

Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx	2019-08-29 22:51:56 UTC (rev 26119)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx	2019-08-29 23:04:36 UTC (rev 26120)
@@ -52,6 +52,7 @@
 addConstraint(new VConstraintSampledFieldSpatialSampledFieldOneSampleIn1DGeometry(*this));
 addConstraint(new VConstraintSampledFieldSpatialSampledFieldTwoSamplesIn2DGeometry(*this));
 addConstraint(new VConstraintSampledFieldSpatialSampledFieldThreeSamplesIn3DGeometry(*this));
+addConstraint(new VConstraintSampledVolumeSpatialSampledVolumeNeedsMaxWithMin(*this));
 
 /** @endcond */
 

Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-01.xml	                        (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-01.xml	2019-08-29 23:04:36 UTC (rev 26120)
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+    <model>
+        <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+            <spatial:listOfCoordinateComponents>
+                <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+                    <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+                    <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+                </spatial:coordinateComponent>
+            </spatial:listOfCoordinateComponents>
+            <spatial:listOfDomainTypes>
+                <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+            </spatial:listOfDomainTypes>
+            <spatial:listOfGeometryDefinitions>
+                <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+                    <spatial:listOfSampledVolumes>
+                        <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0"/>
+                    </spatial:listOfSampledVolumes>
+                </spatial:sampledFieldGeometry>
+            </spatial:listOfGeometryDefinitions>
+            <spatial:listOfSampledFields>
+                <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+            </spatial:listOfSampledFields>
+        </spatial:geometry>
+    </model>
+</sbml>

Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-pass-00-01.xml	                        (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-pass-00-01.xml	2019-08-29 23:04:36 UTC (rev 26120)
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+    <model>
+        <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+            <spatial:listOfCoordinateComponents>
+                <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+                    <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+                    <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+                </spatial:coordinateComponent>
+            </spatial:listOfCoordinateComponents>
+            <spatial:listOfDomainTypes>
+                <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+            </spatial:listOfDomainTypes>
+            <spatial:listOfGeometryDefinitions>
+                <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+                    <spatial:listOfSampledVolumes>
+                        <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="0.5"/>
+                    </spatial:listOfSampledVolumes>
+                </spatial:sampledFieldGeometry>
+            </spatial:listOfGeometryDefinitions>
+            <spatial:listOfSampledFields>
+                <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+            </spatial:listOfSampledFields>
+        </spatial:geometry>
+    </model>
+</sbml>





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

sbml-svn Mailing List for Systems Biology Markup Language (SBML) (Page 9)

A file format for exchanging computational models in systems biology

sbml-svn — SVN commit notification list for the SBML project.