put in some testing for distribution units

sbmlteam · Aug 3, 2024 · ac6bca3 · ac6bca3
1 parent 5b27f56
commit ac6bca3
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Showing 4 changed files with 133 additions and 5 deletions.
diff --git a/src/sbml/packages/distrib/validator/test/TestDistribConsistencyValidator.cpp b/src/sbml/packages/distrib/validator/test/TestDistribConsistencyValidator.cpp
@@ -44,6 +44,7 @@
 
 #include <sbml/packages/distrib/validator/DistribConsistencyValidator.h>
 #include <sbml/packages/distrib/validator/DistribIdentifierConsistencyValidator.h>
+#include <sbml/validator/UnitConsistencyValidator.h>
 
 #ifdef LIBSBML_USE_VLD
   #include <vld.h>
@@ -85,6 +86,21 @@ runIdTest (const TestFile& file)
   TestValidator        tester(validator);
 
 
+  validator.init();
+
+  return tester.test(file);
+}
+/**
+ * @return true if the Validator behaved as expected when validating
+ * TestFile, false otherwise.
+ */
+bool
+runUnitTest (const TestFile& file)
+{
+  UnitConsistencyValidator validator;
+  TestValidator        tester(validator);
+
+
   validator.init();
 
   return tester.test(file);
@@ -164,9 +180,14 @@ main (int argc, char* argv[])
   failed += runTests( "Testing General XML Consistency Constraints (20000 - 29999)",
 		      testThisDataDir, 0, 0, runMainTest, library);
 
-  testThisDataDir = testDataDir + "/" + "identifier-constraints";
-  failed += runTests( "Testing Id Consistency Constraints (10300 - 10399)",
-		      testThisDataDir, 0, 0, runIdTest, library);
+  // commented out as we don't actually have any of these tests
+  //testThisDataDir = testDataDir + "/" + "identifier-constraints";
+  //failed += runTests( "Testing Id Consistency Constraints (10300 - 10399)",
+		//      testThisDataDir, 0, 0, runIdTest, library);
+
+  testThisDataDir = testDataDir + "/" + "unit-constraints";
+  failed += runTests("Testing Unit Consistency Constraints (10500 - 10599)",
+	  testThisDataDir, 0, 0, runUnitTest, library);
 
   return failed;
 }

diff --git a/src/sbml/packages/distrib/validator/test/TestFile.cpp b/src/sbml/packages/distrib/validator/test/TestFile.cpp
@@ -94,8 +94,13 @@ TestFile::getFullname () const
 
 unsigned int
 TestFile::getConstraintId () const
-{
-  return atol( mFilename.substr(0, 7).c_str() );
+{ 
+    unsigned int constraint = atol( mFilename.substr(0, 7).c_str() );
+    if (constraint > 1510500 && constraint < 1510599)
+    {
+        constraint = constraint - 1500000;
+    }
+    return constraint;
 }
 
 

diff --git a/src/sbml/packages/distrib/validator/test/test-data/unit-constraints/1510523-fail-01-01.xml b/src/sbml/packages/distrib/validator/test/test-data/unit-constraints/1510523-fail-01-01.xml
@@ -0,0 +1,102 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" level="3" version="2" comp:required="true" distrib:required="true">
+  <notes>
+    <body xmlns="http://www.w3.org/1999/xhtml">
+      <p>Created with <a href="https://github.com/matthiaskoenig/sbmlutils">https://github.com/matthiaskoenig/sbmlutils</a>.
+<a href="https://doi.org/10.5281/zenodo.5525390">
+        <img src="https://zenodo.org/badge/DOI/10.5281/zenodo.5525390.svg" alt="DOI"/></a></p>
+      </body>
+    </notes>
+  <model id="spt_random" name="Model for testing uniform units" substanceUnits="mmole" timeUnits="min" volumeUnits="litre" areaUnits="m2" lengthUnits="metre" extentUnits="mmole">
+    <listOfUnitDefinitions>
+      <unitDefinition id="g_per_mole" name="g/mole">
+        <listOfUnits>
+          <unit kind="gram" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="l_per_min" name="l/min">
+        <listOfUnits>
+          <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="60"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="m2" name="meter^2">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="mM" name="mmole/liter">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="litre" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="mg" name="mg">
+        <listOfUnits>
+          <unit kind="gram" exponent="1" scale="0" multiplier="0.001"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="mg_per_s_l" name="mg/s/l">
+        <listOfUnits>
+          <unit kind="gram" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="litre" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="min" name="min">
+        <listOfUnits>
+          <unit kind="second" exponent="1" scale="0" multiplier="60"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="min_per_hr" name="min/hour">
+        <listOfUnits>
+          <unit kind="second" exponent="1" scale="0" multiplier="60"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="3600"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="mmole" name="mmole">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="0.001"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="mmole_per_min" name="mmole/min">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="60"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="mmole_per_min_l" name="mmole/min/l">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="60"/>
+          <unit kind="litre" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="per_min" name="1/min">
+        <listOfUnits>
+          <unit kind="second" exponent="-1" scale="0" multiplier="60"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="per_mmole" name="1/mmole">
+        <listOfUnits>
+          <unit kind="mole" exponent="-1" scale="0" multiplier="0.001"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfParameters>
+      <parameter id="protein_random" value="0.5" units="second" constant="true"/>
+    </listOfParameters>
+    <listOfInitialAssignments>
+      <initialAssignment symbol="protein_random">
+        <math xmlns="http://www.w3.org/1998/Math/MathML" xmlns:sbml="http://www.sbml.org/sbml/level3/version2/core">
+          <apply>
+            <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/uniform"> uniform </csymbol>
+            <cn sbml:units="dimensionless" type="integer"> 0 </cn>
+            <cn sbml:units="dimensionless" type="integer"> 1 </cn>
+          </apply>
+        </math>
+      </initialAssignment>
+    </listOfInitialAssignments>
+  </model>
+</sbml>
diff --git a/...test-data/unit-constraints/spt_random.xml → ...a/unit-constraints/1510523-pass-00-01.xml b/...test-data/unit-constraints/spt_random.xml → ...a/unit-constraints/1510523-pass-00-01.xml