void test000068::test_bug1068()
{
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
CPPUNIT_ASSERT(pDataModel->importSBMLFromString(MODEL_STRING1));
CModel* pModel = pDataModel->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->getQuantityUnitEnum() == CUnit::Mol);
CPPUNIT_ASSERT(pModel->getVolumeUnitEnum() == CUnit::l);
CPPUNIT_ASSERT(pModel->getTimeUnitEnum() == CUnit::s);
CPPUNIT_ASSERT(pModel->getCompartments().size() == 1);
const CCompartment* pCompartment = pModel->getCompartments()[0];
CPPUNIT_ASSERT(pCompartment != NULL);
CPPUNIT_ASSERT(pCompartment->getStatus() == CModelEntity::FIXED);
CPPUNIT_ASSERT(pModel->getMetabolites().size() == 6);
// check metabolites
const CMetab* pMetab = pModel->getMetabolites()[0];
CPPUNIT_ASSERT(pMetab != NULL);
CPPUNIT_ASSERT(pMetab->getObjectName() == "A");
CPPUNIT_ASSERT(pMetab->getStatus() == CModelEntity::REACTIONS);
pMetab = pModel->getMetabolites()[1];
CPPUNIT_ASSERT(pMetab != NULL);
CPPUNIT_ASSERT(pMetab->getObjectName() == "B");
CPPUNIT_ASSERT(pMetab->getStatus() == CModelEntity::REACTIONS);
pMetab = pModel->getMetabolites()[2];
CPPUNIT_ASSERT(pMetab != NULL);
CPPUNIT_ASSERT(pMetab->getObjectName() == "C");
CPPUNIT_ASSERT(pMetab->getStatus() == CModelEntity::ASSIGNMENT);
// check assignment
const CEvaluationTree* pTree = pMetab->getExpressionPtr();
CPPUNIT_ASSERT(pTree != NULL);
const CEvaluationNode* pRoot = pTree->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot) != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot)->getData() == "function_5");
pMetab = pModel->getMetabolites()[3];
CPPUNIT_ASSERT(pMetab != NULL);
CPPUNIT_ASSERT(pMetab->getObjectName() == "D");
CPPUNIT_ASSERT(pMetab->getStatus() == CModelEntity::ODE);
// check ode
pTree = pMetab->getExpressionPtr();
CPPUNIT_ASSERT(pTree != NULL);
pRoot = pTree->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot) != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot)->getData() == "function_2");
pMetab = pModel->getMetabolites()[4];
CPPUNIT_ASSERT(pMetab != NULL);
CPPUNIT_ASSERT(pMetab->getObjectName() == "E");
CPPUNIT_ASSERT(pMetab->getStatus() == CModelEntity::ODE);
// check ode
pTree = pMetab->getExpressionPtr();
CPPUNIT_ASSERT(pTree != NULL);
pRoot = pTree->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot) != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot)->getData() == "function_4");
pMetab = pModel->getMetabolites()[5];
CPPUNIT_ASSERT(pMetab != NULL);
CPPUNIT_ASSERT(pMetab->getObjectName() == "F");
CPPUNIT_ASSERT(pMetab->getStatus() == CModelEntity::ODE);
// check ode
pTree = pMetab->getExpressionPtr();
CPPUNIT_ASSERT(pTree != NULL);
pRoot = pTree->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot) != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot)->getData() == "function_6");
// check model values
CPPUNIT_ASSERT(pModel->getModelValues().size() == 3);
const CModelValue* pModelValue = pModel->getModelValues()[0];
CPPUNIT_ASSERT(pModelValue != NULL);
CPPUNIT_ASSERT(pModelValue->getObjectName() == "K1");
CPPUNIT_ASSERT(pModelValue->getStatus() == CModelEntity::ASSIGNMENT);
// check assignment
pTree = pModelValue->getExpressionPtr();
CPPUNIT_ASSERT(pTree != NULL);
pRoot = pTree->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot) != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot)->getData() == "function_1");
pModelValue = pModel->getModelValues()[1];
CPPUNIT_ASSERT(pModelValue != NULL);
CPPUNIT_ASSERT(pModelValue->getObjectName() == "K2");
CPPUNIT_ASSERT(pModelValue->getStatus() == CModelEntity::FIXED);
pModelValue = pModel->getModelValues()[2];
CPPUNIT_ASSERT(pModelValue != NULL);
CPPUNIT_ASSERT(pModelValue->getObjectName() == "K3");
// check assignment
pTree = pModelValue->getExpressionPtr();
CPPUNIT_ASSERT(pTree != NULL);
pRoot = pTree->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot) != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot)->getData() == "function_3");
CPPUNIT_ASSERT(pModel->getReactions().size() == 6);
// check reactions
const CReaction* pReaction = pModel->getReactions()[0];
CPPUNIT_ASSERT(pReaction != NULL);
CPPUNIT_ASSERT(pReaction->getChemEq().getSubstrates().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getProducts().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getModifiers().size() == 0);
CPPUNIT_ASSERT(pReaction->isReversible() == true);
// check the kinetic law
CPPUNIT_ASSERT(pReaction->getParameters().size() == 1);
const CFunction* pFunction = pReaction->getFunction();
CPPUNIT_ASSERT(pFunction != NULL);
CPPUNIT_ASSERT(pFunction->getType() == CEvaluationTree::UserDefined);
CPPUNIT_ASSERT(pFunction->getObjectName() == "Function for reaction1");
pRoot = pFunction->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
pReaction = pModel->getReactions()[1];
CPPUNIT_ASSERT(pReaction != NULL);
CPPUNIT_ASSERT(pReaction->getChemEq().getSubstrates().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getProducts().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getModifiers().size() == 0);
CPPUNIT_ASSERT(pReaction->isReversible() == true);
// check the kinetic law
CPPUNIT_ASSERT(pReaction->getParameters().size() == 2);
pFunction = pReaction->getFunction();
CPPUNIT_ASSERT(pFunction != NULL);
CPPUNIT_ASSERT(pFunction->getType() == CEvaluationTree::UserDefined);
CPPUNIT_ASSERT(pFunction->getObjectName() == "Function for reaction2");
pRoot = pFunction->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
pReaction = pModel->getReactions()[2];
CPPUNIT_ASSERT(pReaction != NULL);
CPPUNIT_ASSERT(pReaction->getChemEq().getSubstrates().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getProducts().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getModifiers().size() == 0);
CPPUNIT_ASSERT(pReaction->isReversible() == true);
// check the kinetic law
CPPUNIT_ASSERT(pReaction->getParameters().size() == 1);
pFunction = pReaction->getFunction();
CPPUNIT_ASSERT(pFunction != NULL);
CPPUNIT_ASSERT(pFunction->getType() == CEvaluationTree::UserDefined);
CPPUNIT_ASSERT(pFunction->getObjectName() == "Function for reaction3");
pRoot = pFunction->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
pReaction = pModel->getReactions()[3];
CPPUNIT_ASSERT(pReaction != NULL);
CPPUNIT_ASSERT(pReaction->getChemEq().getSubstrates().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getProducts().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getModifiers().size() == 0);
CPPUNIT_ASSERT(pReaction->isReversible() == true);
// check the kinetic law
CPPUNIT_ASSERT(pReaction->getParameters().size() == 0);
pFunction = pReaction->getFunction();
CPPUNIT_ASSERT(pFunction != NULL);
CPPUNIT_ASSERT(pFunction->getType() == CEvaluationTree::UserDefined);
CPPUNIT_ASSERT(pFunction->getObjectName() == "Function for reaction4");
pRoot = pFunction->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
pReaction = pModel->getReactions()[4];
CPPUNIT_ASSERT(pReaction != NULL);
CPPUNIT_ASSERT(pReaction->getChemEq().getSubstrates().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getProducts().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getModifiers().size() == 0);
CPPUNIT_ASSERT(pReaction->isReversible() == true);
// check the kinetic law
CPPUNIT_ASSERT(pReaction->getParameters().size() == 2);
pFunction = pReaction->getFunction();
CPPUNIT_ASSERT(pFunction != NULL);
CPPUNIT_ASSERT(pFunction->getType() == CEvaluationTree::UserDefined);
CPPUNIT_ASSERT(pFunction->getObjectName() == "Function for reaction5");
pRoot = pFunction->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
pReaction = pModel->getReactions()[5];
CPPUNIT_ASSERT(pReaction != NULL);
CPPUNIT_ASSERT(pReaction->getChemEq().getSubstrates().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getProducts().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getModifiers().size() == 0);
CPPUNIT_ASSERT(pReaction->isReversible() == true);
// check the kinetic law
CPPUNIT_ASSERT(pReaction->getParameters().size() == 3);
pFunction = pReaction->getFunction();
CPPUNIT_ASSERT(pFunction != NULL);
CPPUNIT_ASSERT(pFunction->getType() == CEvaluationTree::UserDefined);
CPPUNIT_ASSERT(pFunction->getObjectName() == "Function for reaction6");
pRoot = pFunction->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
// export to SBML
std::string s = pDataModel->exportSBMLToString(NULL, 1, 2);
CPPUNIT_ASSERT(s.empty() == false);
// due to the bugfix for Bug 1086 and some issues with libsbml and the current exporter,
// we now no longer have a L1 document in the datamodel if there was an SBMLDocument prior
// to exporting to L1 already.
// To test now, we have to call newModel on the datamodel to delete the old sbml document,
// and reimport the exported model
// This will also lead to a Level 2 Version 1 model since we convert all Level 1 model to
// Level 2 Version 1 on import, but we can at least test if the export worked.
pCOPASIDATAMODEL->newModel(NULL, true);
CPPUNIT_ASSERT(pCOPASIDATAMODEL->importSBMLFromString(s));
// check the sbml model
const SBMLDocument* pDocument = pCOPASIDATAMODEL->getCurrentSBMLDocument();
CPPUNIT_ASSERT(pDocument != NULL);
CPPUNIT_ASSERT(pDocument->getLevel() == 2);
CPPUNIT_ASSERT(pDocument->getVersion() == 1);
const Model* pSBMLModel = pDocument->getModel();
CPPUNIT_ASSERT(pSBMLModel != NULL);
CPPUNIT_ASSERT(pSBMLModel->getListOfFunctionDefinitions()->size() == 0);
CPPUNIT_ASSERT(pSBMLModel->getListOfCompartments()->size() == 1);
CPPUNIT_ASSERT(pSBMLModel->getListOfSpecies()->size() == 6);
CPPUNIT_ASSERT(pSBMLModel->getListOfParameters()->size() == 3);
CPPUNIT_ASSERT(pSBMLModel->getListOfRules()->size() == 6);
CPPUNIT_ASSERT(pSBMLModel->getListOfReactions()->size() == 6);
std::map<std::string, const Rule*> ruleMap;
unsigned int i, iMax = pSBMLModel->getListOfRules()->size();
const Rule* pRule = NULL;
for (i = 0; i < iMax; ++i)
{
pRule = pSBMLModel->getRule(i);
ruleMap.insert(std::pair<std::string, const Rule*>(pRule->getVariable(), pRule));
}
// check the rules
std::map<std::string, const Rule*>::const_iterator pos = ruleMap.find("parameter_1");
CPPUNIT_ASSERT(pos != ruleMap.end());
pRule = pos->second;
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pRule->getVariable() == "parameter_1");
const ASTNode* pMath = pRule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
// only check the infix
std::string formula = pRule->getFormula();
CPPUNIT_ASSERT(formula == "3 * 4.5");
pos = ruleMap.find("parameter_3");
CPPUNIT_ASSERT(pos != ruleMap.end());
pRule = pos->second;
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pRule->getVariable() == "parameter_3");
pRule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
// only check the infix
formula = pRule->getFormula();
CPPUNIT_ASSERT(formula == "parameter_1 - 2 * 1.3");
pos = ruleMap.find("species_3");
CPPUNIT_ASSERT(pos != ruleMap.end());
pRule = pos->second;
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pRule->getVariable() == "species_3");
pRule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
// only check the infix
formula = pRule->getFormula();
CPPUNIT_ASSERT(formula == "parameter_1 - 3.5 * 1.3 + (3 * 2.4 - 5.23)");
pos = ruleMap.find("species_4");
CPPUNIT_ASSERT(pos != ruleMap.end());
pRule = pos->second;
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pRule->getVariable() == "species_4");
pRule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
// only check the infix
formula = pRule->getFormula();
CPPUNIT_ASSERT(formula == "3.4 + parameter_1");
pos = ruleMap.find("species_5");
CPPUNIT_ASSERT(pos != ruleMap.end());
pRule = pos->second;
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pRule->getVariable() == "species_5");
pRule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
// only check the infix
formula = pRule->getFormula();
CPPUNIT_ASSERT(formula == "(parameter_2 + 1.4) / 2");
pos = ruleMap.find("species_6");
CPPUNIT_ASSERT(pos != ruleMap.end());
pRule = pos->second;
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pRule->getVariable() == "species_6");
pRule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
// only check the infix
formula = pRule->getFormula();
CPPUNIT_ASSERT(formula == "parameter_3 - 3.4 * 1.3 + (3 * parameter_1 - 5.23)");
// check the reactions
const Reaction* pSBMLReaction = pSBMLModel->getReaction(0);
CPPUNIT_ASSERT(pSBMLReaction != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getListOfReactants()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfProducts()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfModifiers()->size() == 0);
CPPUNIT_ASSERT(pSBMLReaction->getReversible() == true);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw() != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw()->getListOfParameters()->size() == 0);
pMath = pSBMLReaction->getKineticLaw()->getMath();
CPPUNIT_ASSERT(pMath != NULL);
formula = pSBMLReaction->getKineticLaw()->getFormula();
CPPUNIT_ASSERT(formula == "compartment_1 * 3 * parameter_1");
pSBMLReaction = pSBMLModel->getReaction(1);
CPPUNIT_ASSERT(pSBMLReaction != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getListOfReactants()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfProducts()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfModifiers()->size() == 0);
CPPUNIT_ASSERT(pSBMLReaction->getReversible() == true);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw() != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw()->getListOfParameters()->size() == 0);
pMath = pSBMLReaction->getKineticLaw()->getMath();
CPPUNIT_ASSERT(pMath != NULL);
formula = pSBMLReaction->getKineticLaw()->getFormula();
CPPUNIT_ASSERT(formula == "compartment_1 * (parameter_2 + parameter_1)");
pSBMLReaction = pSBMLModel->getReaction(2);
CPPUNIT_ASSERT(pSBMLReaction != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getListOfReactants()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfProducts()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfModifiers()->size() == 0);
CPPUNIT_ASSERT(pSBMLReaction->getReversible() == true);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw() != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw()->getListOfParameters()->size() == 0);
pMath = pSBMLReaction->getKineticLaw()->getMath();
CPPUNIT_ASSERT(pMath != NULL);
formula = pSBMLReaction->getKineticLaw()->getFormula();
CPPUNIT_ASSERT(formula == "compartment_1 * (species_2 - parameter_1 * 1.3)");
pSBMLReaction = pSBMLModel->getReaction(3);
CPPUNIT_ASSERT(pSBMLReaction != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getListOfReactants()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfProducts()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfModifiers()->size() == 0);
CPPUNIT_ASSERT(pSBMLReaction->getReversible() == true);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw() != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw()->getListOfParameters()->size() == 0);
pMath = pSBMLReaction->getKineticLaw()->getMath();
CPPUNIT_ASSERT(pMath != NULL);
formula = pSBMLReaction->getKineticLaw()->getFormula();
CPPUNIT_ASSERT(formula == "compartment_1 * ((species_2 + species_1) / 2)");
pSBMLReaction = pSBMLModel->getReaction(4);
CPPUNIT_ASSERT(pSBMLReaction != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getListOfReactants()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfProducts()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfModifiers()->size() == 0);
CPPUNIT_ASSERT(pSBMLReaction->getReversible() == true);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw() != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw()->getListOfParameters()->size() == 0);
pMath = pSBMLReaction->getKineticLaw()->getMath();
CPPUNIT_ASSERT(pMath != NULL);
formula = pSBMLReaction->getKineticLaw()->getFormula();
CPPUNIT_ASSERT(formula == "compartment_1 * (parameter_1 - species_2 * 1.3 + (3 * parameter_3 - 5.23))");
pSBMLReaction = pSBMLModel->getReaction(5);
CPPUNIT_ASSERT(pSBMLReaction != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getListOfReactants()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfProducts()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfModifiers()->size() == 0);
CPPUNIT_ASSERT(pSBMLReaction->getReversible() == true);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw() != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw()->getListOfParameters()->size() == 0);
pMath = pSBMLReaction->getKineticLaw()->getMath();
CPPUNIT_ASSERT(pMath != NULL);
formula = pSBMLReaction->getKineticLaw()->getFormula();
CPPUNIT_ASSERT(formula == "compartment_1 * (parameter_1 - parameter_3 * 1.3 + (3 * parameter_2 - 5.23))");
}
void test000009::test_references_to_species()
{
// load the CPS file
// export to SBML
// check the resulting SBML model
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
std::istringstream iss(test000009::MODEL_STRING);
CPPUNIT_ASSERT(load_cps_model_from_stream(iss, *pDataModel) == true);
CPPUNIT_ASSERT(pDataModel->getModel() != NULL);
CPPUNIT_ASSERT(pDataModel->exportSBMLToString(NULL, 2, 3).empty() == false);
SBMLDocument* pDocument = pDataModel->getCurrentSBMLDocument();
CPPUNIT_ASSERT(pDocument != NULL);
Model* pModel = pDocument->getModel();
CPPUNIT_ASSERT(pModel != NULL);
// assert that there is only one compartment and
// assert the compartment is constant
CPPUNIT_ASSERT(pModel->getNumCompartments() == 1);
Compartment* pCompartment = pModel->getCompartment(0);
CPPUNIT_ASSERT(pCompartment->getConstant() == false);
CPPUNIT_ASSERT(pModel->getNumSpecies() == 2);
Species* pSpecies = pModel->getSpecies(1);
CPPUNIT_ASSERT(pSpecies->getHasOnlySubstanceUnits() == true);
pSpecies = pModel->getSpecies(0);
std::string idSpeciesA = pSpecies->getId();
CPPUNIT_ASSERT(pSpecies->getHasOnlySubstanceUnits() == true);
CPPUNIT_ASSERT(pModel->getNumRules() == 2);
// there are two rules, one is the rule for the compartment
AssignmentRule* pRule = dynamic_cast<AssignmentRule*>(pModel->getRule(0));
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pModel->getNumParameters() == 1);
Parameter* pParameter = pModel->getParameter(0);
CPPUNIT_ASSERT(pParameter != NULL);
if (pRule->getVariable() != pParameter->getId())
{
pRule = dynamic_cast<AssignmentRule*>(pModel->getRule(1));
}
CPPUNIT_ASSERT(pRule->getVariable() == pParameter->getId());
const ASTNode* pMath = pRule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
// the expression should be the species divided by the volume
CPPUNIT_ASSERT(pMath->getType() == AST_DIVIDE);
CPPUNIT_ASSERT(pMath->getChild(0) != NULL);
CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getChild(0)->getName() == pSpecies->getId());
CPPUNIT_ASSERT(pMath->getChild(1) != NULL);
CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getChild(1)->getName() == pCompartment->getId());
CPPUNIT_ASSERT(pModel->getNumReactions() == 2);
Reaction* pReaction = pModel->getReaction(0);
// make sure this is reaction A ->
CPPUNIT_ASSERT(pReaction != NULL);
CPPUNIT_ASSERT(pReaction->getNumReactants() == 1);
CPPUNIT_ASSERT(pReaction->getNumProducts() == 0);
// check if all references in the kinetic law are unmodified
// math element must be a multiplication of the mass action term by
// the compartment volume
// the mass action term is a multiplication of the parameter node by
// the species node
// the code that multiplies the reaction by the compartments volume
// recognizes the division of the species by the compartment and cancels
// those two
CPPUNIT_ASSERT(pReaction->isSetKineticLaw() == true);
KineticLaw* pLaw = pReaction->getKineticLaw();
CPPUNIT_ASSERT(pLaw != NULL);
CPPUNIT_ASSERT(pLaw->isSetMath() == true);
pMath = pLaw->getMath();
CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getChild(0)->getName() == std::string("k1"));
CPPUNIT_ASSERT(pMath->getChild(1) != NULL);
CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getChild(1)->getName() == idSpeciesA);
pReaction = pModel->getReaction(1);
// make sure this is reaction A -> S
CPPUNIT_ASSERT(pReaction != NULL);
CPPUNIT_ASSERT(pReaction->getNumReactants() == 1);
CPPUNIT_ASSERT(pReaction->getNumProducts() == 1);
// check if all references in the kinetic law are unmodified
// math element must be a multiplication of the compartments volume with
// a function call with three arguments
// the first argument is the reference to the species
CPPUNIT_ASSERT(pReaction->isSetKineticLaw() == true);
pLaw = pReaction->getKineticLaw();
CPPUNIT_ASSERT(pLaw != NULL);
CPPUNIT_ASSERT(pLaw->isSetMath() == true);
pMath = pLaw->getMath();
CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getChild(0)->getName() == pCompartment->getId());
pMath = pMath->getChild(1);
CPPUNIT_ASSERT(pMath != NULL);
CPPUNIT_ASSERT(pMath->getType() == AST_FUNCTION);
CPPUNIT_ASSERT(pMath->getNumChildren() == 3);
pMath = pMath->getChild(0);
CPPUNIT_ASSERT(pMath != NULL);
CPPUNIT_ASSERT(pMath->getType() == AST_DIVIDE);
CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
CPPUNIT_ASSERT(pMath->getChild(0) != NULL);
CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getChild(0)->getName() == idSpeciesA);
CPPUNIT_ASSERT(pMath->getChild(1) != NULL);
CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getChild(1)->getName() == pCompartment->getId());
}
void test000054::test_bug1002()
{
// load the CPS file
// export to SBML
// check the resulting SBML model
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
std::istringstream iss(test000054::MODEL_STRING);
CPPUNIT_ASSERT(load_cps_model_from_stream(iss, *pDataModel) == true);
CPPUNIT_ASSERT(pDataModel->getModel() != NULL);
CPPUNIT_ASSERT(pDataModel->exportSBMLToString(NULL, 2, 3).empty() == false);
SBMLDocument* pDocument = pDataModel->getCurrentSBMLDocument();
CPPUNIT_ASSERT(pDocument != NULL);
Model* pSBMLModel = pDocument->getModel();
CPPUNIT_ASSERT(pSBMLModel != NULL);
CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 0);
CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 0);
CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 0);
CPPUNIT_ASSERT(pSBMLModel->getNumInitialAssignments() == 0);
CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 5);
const Parameter* pParameter1 = pSBMLModel->getParameter(0);
CPPUNIT_ASSERT(pParameter1 != NULL);
CPPUNIT_ASSERT(pParameter1->getConstant() == false);
const Parameter* pParameter2 = pSBMLModel->getParameter(1);
CPPUNIT_ASSERT(pParameter2 != NULL);
CPPUNIT_ASSERT(pParameter2->getConstant() == false);
const Parameter* pParameter3 = pSBMLModel->getParameter(2);
CPPUNIT_ASSERT(pParameter3 != NULL);
CPPUNIT_ASSERT(pParameter3->getConstant() == false);
const Parameter* pParameter4 = pSBMLModel->getParameter(3);
CPPUNIT_ASSERT(pParameter4 != NULL);
CPPUNIT_ASSERT(pParameter4->getConstant() == false);
const Parameter* pParameter5 = pSBMLModel->getParameter(4);
CPPUNIT_ASSERT(pParameter5 != NULL);
CPPUNIT_ASSERT(pParameter5->getConstant() == false);
CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 5);
const Rule* pRule = pSBMLModel->getRule(0);
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pRule->getTypeCode() == SBML_ASSIGNMENT_RULE);
const AssignmentRule* pARule = dynamic_cast<const AssignmentRule*>(pRule);
CPPUNIT_ASSERT(pARule != NULL);
CPPUNIT_ASSERT(pARule->getVariable() == pParameter4->getId());
CPPUNIT_ASSERT(pARule->isSetMath() == true);
const ASTNode* pMath = pARule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
CPPUNIT_ASSERT(pMath->getType() == AST_PLUS);
CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
const ASTNode* pChild1 = pMath->getChild(0);
CPPUNIT_ASSERT(pChild1 != NULL);
CPPUNIT_ASSERT(pChild1->getType() == AST_REAL);
CPPUNIT_ASSERT(fabs((pChild1->getReal() - 2.0) / 2.0) < 1e-15);
const ASTNode* pChild2 = pMath->getChild(1);
CPPUNIT_ASSERT(pChild2 != NULL);
CPPUNIT_ASSERT(pChild2->getType() == AST_REAL);
CPPUNIT_ASSERT(fabs((pChild2->getReal() - 4.0) / 4.0) < 1e-15);
pRule = pSBMLModel->getRule(1);
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pRule->getTypeCode() == SBML_ASSIGNMENT_RULE);
pARule = dynamic_cast<const AssignmentRule*>(pRule);
CPPUNIT_ASSERT(pARule != NULL);
CPPUNIT_ASSERT(pARule->getVariable() == pParameter1->getId());
CPPUNIT_ASSERT(pARule->isSetMath() == true);
pMath = pARule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
CPPUNIT_ASSERT(pMath->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getName() == pParameter4->getId());
CPPUNIT_ASSERT(pMath->getNumChildren() == 0);
pRule = pSBMLModel->getRule(2);
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pRule->getTypeCode() == SBML_ASSIGNMENT_RULE);
pARule = dynamic_cast<const AssignmentRule*>(pRule);
CPPUNIT_ASSERT(pARule != NULL);
CPPUNIT_ASSERT(pARule->getVariable() == pParameter3->getId());
CPPUNIT_ASSERT(pARule->isSetMath() == true);
pMath = pARule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
CPPUNIT_ASSERT(pMath->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getName() == pParameter1->getId());
CPPUNIT_ASSERT(pMath->getNumChildren() == 0);
pRule = pSBMLModel->getRule(3);
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pRule->getTypeCode() == SBML_ASSIGNMENT_RULE);
pARule = dynamic_cast<const AssignmentRule*>(pRule);
CPPUNIT_ASSERT(pARule != NULL);
CPPUNIT_ASSERT(pARule->getVariable() == pParameter5->getId());
CPPUNIT_ASSERT(pARule->isSetMath() == true);
pMath = pARule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
CPPUNIT_ASSERT(pMath->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getName() == pParameter3->getId());
CPPUNIT_ASSERT(pMath->getNumChildren() == 0);
pRule = pSBMLModel->getRule(4);
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pRule->getTypeCode() == SBML_ASSIGNMENT_RULE);
pARule = dynamic_cast<const AssignmentRule*>(pRule);
CPPUNIT_ASSERT(pARule != NULL);
CPPUNIT_ASSERT(pARule->getVariable() == pParameter2->getId());
CPPUNIT_ASSERT(pARule->isSetMath() == true);
pMath = pARule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
CPPUNIT_ASSERT(pMath->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getName() == pParameter5->getId());
CPPUNIT_ASSERT(pMath->getNumChildren() == 0);
}
