Merge pull request #350 from sbmlteam/fbcV3-update

Update Fbc V3 package
sbmlteam · Sep 19, 2023 · 9faec63 · 9faec63
2 parents bee0af7 + aee04c3
commit 9faec63
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Showing 39 changed files with 892 additions and 197 deletions.
diff --git a/NEWS.txt b/NEWS.txt
@@ -14,6 +14,11 @@ and converting models.
   - Attributes of the ModelHistory can now be accessed from 
     const objects. 
 
+  - The FBC V3 package has been updated to reflect the latest
+    specification. There are now optional attributes `fbc:reaction2` 
+    on the FluxObjective and `fbc:variable2` on the 
+    UserDefinedConstraintComponent.
+
 * Bug fixes
 
   - A bug converting / validating models with the 'comp' package
@@ -23,6 +28,11 @@ and converting models.
 
   - A fix to the CMake Build system ensures that check for dependencies
     is more robust. Thanks to first time contributor @adelhpour
+
+  - The type of the FBC V3 `coefficient` attribute on the 
+    UserDefinedConstraintComponent has been corrected, it was mistakenly
+    a double before, now it has been corrected to be a SIdRef as 
+    described in the specification.
 
 
 ====================================================================

diff --git a/dev/packages/deviser-fbc_v3.xml b/dev/packages/deviser-fbc_v3.xml
@@ -168,6 +168,7 @@
             <attribute name="id" required="false" type="SId" abstract="false"/>
             <attribute name="name" required="false" type="string" abstract="false"/>
             <attribute name="reaction" required="true" type="SIdRef" element="Reaction" abstract="false"/>
+            <attribute name="reaction2" required="false" type="SIdRef" element="Reaction" abstract="false"/>
             <attribute name="coefficient" required="true" type="double" abstract="false"/>
             <attribute name="variableType" required="true" type="enum" element="FbcVariableType" abstract="false"/>
           </attributes>
@@ -226,8 +227,9 @@
           <attributes>
             <attribute name="id" required="false" type="SId" abstract="false"/>
             <attribute name="name" required="false" type="string" abstract="false"/>
-            <attribute name="coefficient" required="true" type="double" abstract="false"/>
+            <attribute name="coefficient" required="true" type="SIdRef" element="Parameter" abstract="false"/>
             <attribute name="variable" required="true" type="SIdRef" element="Reaction,Parameter" abstract="false"/>
+            <attribute name="variable2" required="false" type="SIdRef" element="Reaction,Parameter" abstract="false"/>
             <attribute name="variableType" required="true" type="enum" element="FbcVariableType" abstract="false"/>
           </attributes>
         </element>

diff --git a/src/bindings/matlab/getDefaultValues.m b/src/bindings/matlab/getDefaultValues.m
@@ -3565,7 +3565,7 @@
         int32(-1), ...
         '', ...
         '', ...
-        0/0, ...
+        '', ...
         int32(0), ...
         '', ...
         '', ...

diff --git a/src/bindings/matlab/getValueType.m b/src/bindings/matlab/getValueType.m
@@ -3568,7 +3568,7 @@
         'int', ...
         'char', ...
         'char', ...
-        'double', ...
+        'char', ...
         'bool', ...
         'char', ...
         'char', ...

diff --git a/src/bindings/matlab/test/test-data/fbcV3.xml b/src/bindings/matlab/test/test-data/fbcV3.xml
@@ -75,7 +75,7 @@
     <fbc:listOfUserDefinedConstraints>
       <fbc:userDefinedConstraint sboTerm="SBO:0000001" fbc:id="uc2" fbc:lowerBound="uc2lb" fbc:upperBound="uc2ub">
         <fbc:listOfUserDefinedConstraintComponents>
-          <fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:id="dd" fbc:name="string" fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:id="dd" fbc:name="string" fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>

diff --git a/src/bindings/matlab/test/testReadFromFileFbc3.m b/src/bindings/matlab/test/testReadFromFileFbc3.m
@@ -77,8 +77,8 @@
 
   Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).typecode, 'SBML_FBC_USERDEFINEDCONSTRAINTCOMPONENT'));
   Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_id, 'dd'));
-  Totalfail = Totalfail + fail_unless( m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_coefficient == 2);
   Totalfail = Totalfail + fail_unless( m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).isSetfbc_coefficient == 1);
+  Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_coefficient, 'uc2ub'));
   Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_variable, 'R2'));
   Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_variableType, 'linear'));
 

diff --git a/src/sbml/packages/fbc/extension/test/TestWriteFbcExtension.cpp b/src/sbml/packages/fbc/extension/test/TestWriteFbcExtension.cpp
@@ -415,17 +415,19 @@ START_TEST(test_FbcExtension_create_and_write_L3V1V3)
   FluxObjective* fluxObjective = objective->createFluxObjective();
   fluxObjective->setReaction("J0");
   fluxObjective->setCoefficient(1);
-  fluxObjective->setVariableType("linear");
+  fluxObjective->setReaction2("J0");
+  fluxObjective->setVariableType("quadratic");
 
   UserDefinedConstraint* userconstraint = mplugin->createUserDefinedConstraint();
   userconstraint->setId("uc2");
   userconstraint->setLowerBound("uc2lb");
   userconstraint->setUpperBound("uc2ub");
 
   UserDefinedConstraintComponent * udcc = userconstraint->createUserDefinedConstraintComponent();
-  udcc->setCoefficient(2);
+  udcc->setCoefficient("ucc1");
   udcc->setVariable("Avar");
-  udcc->setVariableType("linear");
+  udcc->setVariableType("quadratic");
+  udcc->setVariable2("Avar2");
 
   // check annotations on several types
   FbcSBasePlugin* sbaseplugin = dynamic_cast<FbcSBasePlugin*>(compartment->getPlugin("fbc"));

diff --git a/src/sbml/packages/fbc/extension/test/test-data/fbc_example2_v3.xml b/src/sbml/packages/fbc/extension/test/test-data/fbc_example2_v3.xml
@@ -32,14 +32,14 @@
           </listOfKeyValuePairs>
         </annotation>
         <fbc:listOfFluxObjectives>
-          <fbc:fluxObjective fbc:reaction="J0" fbc:coefficient="1" fbc:variableType="linear"/>
+          <fbc:fluxObjective fbc:reaction="J0" fbc:coefficient="1" fbc:variableType="quadratic" fbc:reaction2="J0"/>
         </fbc:listOfFluxObjectives>
       </fbc:objective>
     </fbc:listOfObjectives>
     <fbc:listOfUserDefinedConstraints>
       <fbc:userDefinedConstraint fbc:id="uc2" fbc:lowerBound="uc2lb" fbc:upperBound="uc2ub">
         <fbc:listOfUserDefinedConstraintComponents>
-          <fbc:userDefinedConstraintComponent fbc:coefficient="2" fbc:variable="Avar" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent fbc:coefficient="ucc1" fbc:variable="Avar" fbc:variableType="quadratic" fbc:variable2="Avar2"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>

diff --git a/src/sbml/packages/fbc/extension/test/test-data/fbc_examplev3.xml b/src/sbml/packages/fbc/extension/test/test-data/fbc_examplev3.xml
@@ -21,14 +21,14 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent fbc:coefficient="2" fbc:variable="Avar" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent fbc:coefficient="uc2ub" fbc:variable="Avar" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  
     <fbc:listOfObjectives fbc:activeObjective="obj1">
       <fbc:objective fbc:id="obj1" fbc:type="maximize">
         <fbc:listOfFluxes>
-          <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1" fbc:variableType="linear"/>
+          <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1" fbc:variableType="quadratic" fbc:reaction2="J8"/>
         </fbc:listOfFluxes>
       </fbc:objective>
     </fbc:listOfObjectives>