Update Fbc V3 package

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.
 
 
 ====================================================================

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"));

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>

src/sbml/packages/fbc/extension/test/test-data/fbc_examplev3.xml

@@ -28,7 +28,7 @@
     <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>

src/sbml/packages/fbc/sbml/FluxObjective.cpp

@@ -69,6 +69,7 @@ FluxObjective::FluxObjective (unsigned int level, unsigned int version, unsigned
   , mCoefficient (numeric_limits<double>::quiet_NaN())
   , mIsSetCoefficient (false)
   , mVariableType (FBC_VARIABLE_TYPE_INVALID)
+  , mReaction2 ("")
 {
   // set an SBMLNamespaces derived object of this package
   setSBMLNamespacesAndOwn(new FbcPkgNamespaces(level, version, pkgVersion));
@@ -86,6 +87,7 @@ FluxObjective::FluxObjective (FbcPkgNamespaces* fbcns)
   , mCoefficient (numeric_limits<double>::quiet_NaN())
   , mIsSetCoefficient (false)
   , mVariableType (FBC_VARIABLE_TYPE_INVALID)
+  , mReaction2 ("")
 {
   // set the element namespace of this object
   setElementNamespace(fbcns->getURI());
@@ -104,6 +106,7 @@ FluxObjective::FluxObjective(const FluxObjective& orig)
   , mCoefficient ( orig.mCoefficient )
   , mIsSetCoefficient ( orig.mIsSetCoefficient )
   , mVariableType ( orig.mVariableType )
+  , mReaction2 (orig.mReaction2)
 {
 }
 
@@ -123,6 +126,7 @@ FluxObjective::operator=(const FluxObjective& rhs)
     mCoefficient  = rhs.mCoefficient;
     mIsSetCoefficient  = rhs.mIsSetCoefficient;
     mVariableType = rhs.mVariableType;
+    mReaction2  = rhs.mReaction2;
   }
   return *this;
 }
@@ -176,6 +180,16 @@ FluxObjective::getReaction() const
 }
 
 
+/*
+ * Returns the value of the "reaction2" attribute of this FluxObjective.
+ */
+const std::string&
+FluxObjective::getReaction2() const
+{
+  return mReaction2;
+}
+
+
 /*
  * Returns the value of the "coefficient" attribute of this FluxObjective.
  */
@@ -238,6 +252,16 @@ FluxObjective::isSetReaction() const
 }
 
 
+/*
+ * Predicate returning @c true if this FluxObjective's "reaction2" attribute is
+ * set.
+ */
+bool
+FluxObjective::isSetReaction2() const
+{
+  return (mReaction2.empty() == false);
+}
+
 /*
  * Predicate returning @c true if this FluxObjective's "coefficient" attribute
  * is set.
@@ -287,7 +311,17 @@ FluxObjective::setName(const std::string& name)
 int
 FluxObjective::setReaction(const std::string& reaction)
 {
-  return SyntaxChecker::checkAndSetSId(reaction ,mReaction);
+  return SyntaxChecker::checkAndSetSId(reaction, mReaction);
+}
+
+
+/*
+ * Sets reaction2 and returns value indicating success.
+ */
+int
+FluxObjective::setReaction2(const std::string& reaction)
+{
+  return SyntaxChecker::checkAndSetSId(reaction, mReaction2);
 }
 
 
@@ -418,6 +452,25 @@ FluxObjective::unsetReaction()
 }
 
 
+/*
+ * Unsets reaction and returns value indicating success.
+ */
+int
+FluxObjective::unsetReaction2()
+{
+  mReaction2.erase();
+
+  if (mReaction2.empty() == true)
+  {
+    return LIBSBML_OPERATION_SUCCESS;
+  }
+  else
+  {
+    return LIBSBML_OPERATION_FAILED;
+  }
+}
+
+
 /*
  * Unsets coefficient and returns value indicating success.
  */
@@ -460,6 +513,10 @@ FluxObjective::renameSIdRefs(const std::string& oldid, const std::string& newid)
   {
     setReaction(newid);
   }
+  if (isSetReaction2() == true && mReaction2 == oldid)
+  {
+    setReaction2(newid);
+  }
 
 }
 
@@ -697,7 +754,12 @@ FluxObjective::getAttribute(const std::string& attributeName,
     value = getVariableTypeAsString();
     return_value = LIBSBML_OPERATION_SUCCESS;
   }
-
+  else if (attributeName == "reaction2")
+  {
+    value = getReaction2();
+    return_value = LIBSBML_OPERATION_SUCCESS;
+  }
+
   return return_value;
 }
 
@@ -736,6 +798,10 @@ FluxObjective::isSetAttribute(const std::string& attributeName) const
   {
     value = isSetVariableType();
   }
+  else if (attributeName == "reaction2")
+  {
+    value = isSetReaction2();
+  }
 
   return value;
 }
@@ -845,6 +911,10 @@ FluxObjective::setAttribute(const std::string& attributeName,
   {
     return_value = setVariableType(value);
   }
+  else if (attributeName == "reaction2")
+  {
+    return_value = setReaction2(value);
+  }
 
   return return_value;
 }
@@ -883,6 +953,10 @@ FluxObjective::unsetAttribute(const std::string& attributeName)
   {
     value = unsetVariableType();
   }
+  else if (attributeName == "reaction2")
+  {
+    value = unsetReaction2();
+  }
 
   return value;
 }
@@ -912,6 +986,7 @@ FluxObjective::addExpectedAttributes(ExpectedAttributes& attributes)
   if (level == 3 && coreVersion == 1 && pkgVersion == 3)
   {
     attributes.add("variableType");
+    attributes.add("reaction2");
   }
 }
 
@@ -1052,6 +1127,17 @@ FluxObjective::readAttributes (const XMLAttributes& attributes,
   }
 
 
+  assigned = attributes.readInto("reaction2", mReaction2);
+  if (assigned && !SyntaxChecker::isValidSBMLSId(mReaction2))
+  {
+    //
+    // Logs an error if the "id" attribute doesn't
+    // conform to the SBML type SId.
+    //
+    log->logPackageError("fbc", FbcFluxObjectReactionMustBeSIdRef,
+      getPackageVersion(), sbmlLevel, sbmlVersion, "", getLine(), getColumn());
+  }
+
   unsigned int numErrs = log->getNumErrors();
   mIsSetCoefficient = attributes.readInto("coefficient", mCoefficient, log);
 
@@ -1153,6 +1239,9 @@ FluxObjective::writeAttributes (XMLOutputStream& stream) const
       FbcVariableType_toString(mVariableType));
   }
 
+  if (isSetReaction2() == true)
+    stream.writeAttribute("reaction2", getPrefix(), mReaction2);
+
   //
   // (EXTENSION)
   //
@@ -1542,6 +1631,13 @@ FluxObjective_getVariableTypeAsString(const FluxObjective_t * fo)
   return (char*)(FbcVariableType_toString(fo->getVariableType()));
 }
 
+LIBSBML_EXTERN
+const char *
+FluxObjective_getReaction2(const FluxObjective_t * fo)
+{
+  return (fo != NULL && fo->isSetReaction2()) ? fo->getReaction2().c_str() : NULL;
+}
+
 
 LIBSBML_EXTERN
 int
@@ -1583,6 +1679,14 @@ FluxObjective_isSetVariableType(const FluxObjective_t * fo)
 }
 
 
+LIBSBML_EXTERN
+int
+FluxObjective_isSetReaction2(const FluxObjective_t * fo)
+{
+  return (fo != NULL) ? static_cast<int>(fo->isSetReaction2()) : 0;
+}
+
+
 /*
  * Sets the value of the "id" attribute of this FluxObjective_t.
  */
@@ -1652,6 +1756,18 @@ FluxObjective_setVariableTypeAsString(FluxObjective_t * fo,
     LIBSBML_INVALID_OBJECT;
 }
 
+
+LIBSBML_EXTERN
+int
+FluxObjective_setReaction2(FluxObjective_t * fo, const char * reaction)
+{
+  if (fo != NULL)
+    return (reaction == NULL) ? fo->setReaction2("") : fo->setReaction2(reaction);
+  else
+    return LIBSBML_INVALID_OBJECT;
+}
+
+
 LIBSBML_EXTERN
 int
 FluxObjective_unsetId(FluxObjective_t * fo)
@@ -1695,6 +1811,14 @@ FluxObjective_unsetVariableType(FluxObjective_t * fo)
 }
 
 
+LIBSBML_EXTERN
+int
+FluxObjective_unsetReaction2(FluxObjective_t * fo)
+{
+  return (fo != NULL) ? fo->unsetReaction2() : LIBSBML_INVALID_OBJECT;
+}
+
+
 LIBSBML_EXTERN
 int
 FluxObjective_hasRequiredAttributes(const FluxObjective_t * fo)