- fix validation of coefficient

sbmlteam · Sep 15, 2023 · 876212b · 876212b
1 parent 5a54f15
commit 876212b
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Showing 22 changed files with 25 additions and 24 deletions.
diff --git a/src/sbml/packages/fbc/sbml/UserDefinedConstraintComponent.cpp b/src/sbml/packages/fbc/sbml/UserDefinedConstraintComponent.cpp
@@ -1254,13 +1254,14 @@ UserDefinedConstraintComponent::readL3V1V3Attributes(const XMLAttributes&
   // 
 
   numErrs = log ? log->getNumErrors() : 0;
-  assigned = attributes.readInto("coefficient", mCoefficient);
+  XMLTriple tripleCOEFF("coefficient", mURI, getPrefix());
+  assigned = attributes.readInto(tripleCOEFF, mCoefficient);
 
   if (assigned == true)
   {
-    if (mId.empty() == true)
+    if (mCoefficient.empty() == true)
     {
-      logEmptyString(mCoefficient, level, version, "<UserDefinedConstraintComponent>");
+      logEmptyString("coefficient", level, version, "<UserDefinedConstraintComponent>");
     }
     else if (SyntaxChecker::isValidSBMLSId(mCoefficient) == false)
     {

diff --git a/...eneral-constraints/2021304-fail-01-01.xml → ...eneral-constraints/2010302-fail-01-01.xml b/...eneral-constraints/2021304-fail-01-01.xml → ...eneral-constraints/2010302-fail-01-01.xml
@@ -80,7 +80,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent metaid="_udc1" fbc:id="dd" fbc:name="string" sboTerm="SBO:0000001" fbc:coefficient="string" fbc:variable="R2" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent metaid="_udc1" fbc:id="dd" fbc:name="string" sboTerm="SBO:0000001" fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020206-fail-01-05.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020206-fail-01-05.xml
@@ -80,7 +80,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020213-pass-00-01.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020213-pass-00-01.xml
@@ -80,7 +80,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020214-fail-01-01.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020214-fail-01-01.xml
@@ -80,7 +80,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020214-pass-00-01.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020214-pass-00-01.xml
@@ -80,7 +80,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021301-pass-00-01.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021301-pass-00-01.xml
@@ -80,7 +80,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear">
+          <fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear">
           </fbc:userDefinedConstraintComponent>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021302-pass-00-01.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021302-pass-00-01.xml
@@ -80,7 +80,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear">
+          <fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear">
           <annotation/>
           </fbc:userDefinedConstraintComponent>
         </fbc:listOfUserDefinedConstraintComponents>

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021303-fail-01-01.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021303-fail-01-01.xml
@@ -80,7 +80,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent metaid="_udc1" fbc:id="dd" fbc:upperBound="string" sboTerm="SBO:0000001" fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent metaid="_udc1" fbc:id="dd" fbc:upperBound="string" sboTerm="SBO:0000001" fbc:coefficient="uc2ub2" fbc:variable="R2" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021303-pass-00-01.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021303-pass-00-01.xml
@@ -80,7 +80,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent metaid="_udc1" fbc:id="dd" fbc:name="string" sboTerm="SBO:0000001" fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent metaid="_udc1" fbc:id="dd" fbc:name="string" sboTerm="SBO:0000001" fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021305-fail-01-01.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021305-fail-01-01.xml
@@ -80,7 +80,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent fbc:coefficient="2" fbc:variable="RNot" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent fbc:coefficient="uc2ub" fbc:variable="RNot" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021305-pass-00-01.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021305-pass-00-01.xml
@@ -81,7 +81,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021305-pass-00-02.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021305-pass-00-02.xml
@@ -81,7 +81,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent fbc:coefficient="2" fbc:variable="P1" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent fbc:coefficient="uc2ub" fbc:variable="P1" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021306-fail-01-01.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021306-fail-01-01.xml
@@ -81,7 +81,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent fbc:coefficient="2" fbc:variable="P1" fbc:variableType="wrong"/>
+          <fbc:userDefinedConstraintComponent fbc:coefficient="uc2ub" fbc:variable="P1" fbc:variableType="wrong"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021306-pass-00-01.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021306-pass-00-01.xml
@@ -81,7 +81,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent fbc:coefficient="2" fbc:variable="P1" fbc:variableType="quadratic"/>
+          <fbc:userDefinedConstraintComponent fbc:coefficient="uc2ub" fbc:variable="P1" fbc:variableType="quadratic"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021401-pass-00-01.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021401-pass-00-01.xml
@@ -80,7 +80,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021403-fail-01-01.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021403-fail-01-01.xml
@@ -80,7 +80,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021403-fail-01-02.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021403-fail-01-02.xml
@@ -80,7 +80,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021405-fail-01-01.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021405-fail-01-01.xml
@@ -81,7 +81,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021406-fail-01-01.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021406-fail-01-01.xml
@@ -80,7 +80,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021408-pass-00-01.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021408-pass-00-01.xml
@@ -81,7 +81,7 @@
         <annotation/>
         <fbc:listOfUserDefinedConstraintComponents>
 
-          <fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>  

diff --git a/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021409-fail-01-01.xml b/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2021409-fail-01-01.xml
@@ -80,7 +80,7 @@
 
         <fbc:listOfUserDefinedConstraintComponents metaid="__hhh" unitt="mole">
 
-          <fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>