// test whether exporting an SBML Level 3 file after an SBML Level 2 file
// succeeds
void test000100::test_bug1692_1()
{
CPPUNIT_ASSERT(pDataModel != NULL);
std::istringstream iss(test000100::CPS_STRING);
CPPUNIT_ASSERT(load_cps_model_from_stream(iss, *pDataModel) == true);
std::string s;
try
{
s = pDataModel->exportSBMLToString(NULL, 2, 1);
}
catch (...)
{
CPPUNIT_ASSERT_MESSAGE("The first export to Level 2 Version 1 failed.", false);
}
try
{
s = pDataModel->exportSBMLToString(NULL, 3, 1);
}
catch (...)
{
CPPUNIT_ASSERT_MESSAGE("The second export to Level 3 Version 1 failed.", false);
}
}
void test000081::test_bug1205()
{
CDataModel* pDataModel = pCOPASIDATAMODEL;
std::istringstream iss(test000081::MODEL_STRING1);
CPPUNIT_ASSERT(load_cps_model_from_stream(iss, *pDataModel) == true);
CPPUNIT_ASSERT(pDataModel->getModel() != NULL);
const SBMLDocument* pDocument = pDataModel->getCurrentSBMLDocument();
CPPUNIT_ASSERT(pDocument == NULL);
std::string sbmlString;
try
{
sbmlString = pDataModel->exportSBMLToString(NULL, 2, 1);
}
catch (...)
{
// fail if an uncaught exception occurs during export
CPPUNIT_ASSERT(false);
}
CPPUNIT_ASSERT(!sbmlString.empty());
// check if the exported SBML model has three compartments
pDocument = pDataModel->getCurrentSBMLDocument();
CPPUNIT_ASSERT(pDocument != NULL);
const Model* pModel = pDocument->getModel();
CPPUNIT_ASSERT(pModel != NULL);
unsigned int iMax = pModel->getListOfCompartments()->size();
CPPUNIT_ASSERT(iMax == 3);
// check that the compartment named compartment_2 has the id compartment_1
const Compartment* pCompartment = pModel->getCompartment("compartment_1");
CPPUNIT_ASSERT(pCompartment != NULL);
CPPUNIT_ASSERT(pCompartment->getName() == "compartment_2");
// check if the exported SBML model has three species
iMax = pModel->getListOfSpecies()->size();
CPPUNIT_ASSERT(iMax == 3);
// check that the species named species_2 has the id species_1
const Species* pSpecies = pModel->getSpecies("species_1");
CPPUNIT_ASSERT(pSpecies != NULL);
CPPUNIT_ASSERT(pSpecies->getName() == "species_2");
// check if the exported SBML model has three parameters
iMax = pModel->getListOfParameters()->size();
CPPUNIT_ASSERT(iMax == 3);
// check that the parameter named quantity_2 has the id parameter_1
const Parameter* pParameter = pModel->getParameter("parameter_1");
CPPUNIT_ASSERT(pParameter != NULL);
CPPUNIT_ASSERT(pParameter->getName() == "quantity_2");
// check if the exported SBML model has three reactions
iMax = pModel->getListOfReactions()->size();
CPPUNIT_ASSERT(iMax == 3);
// check that the reaction named reaction_2 has the id reaction_1
const Reaction* pReaction = pModel->getReaction("reaction_1");
CPPUNIT_ASSERT(pReaction != NULL);
CPPUNIT_ASSERT(pReaction->getName() == "reaction_2");
}
void test000087::test_export_reaction_flux_reference_1()
{
try
{
std::istringstream iss(test000087::MODEL_STRING4);
bool result = load_cps_model_from_stream(iss, *pCOPASIDATAMODEL);
CPPUNIT_ASSERT(result == true);
CPPUNIT_ASSERT(pCOPASIDATAMODEL->getModel() != NULL);
}
catch (...)
{
// there should be no exception
CPPUNIT_ASSERT(false);
}
try
{
CPPUNIT_ASSERT(pCOPASIDATAMODEL->exportSBMLToString(NULL, 2, 3).empty() == false);
}
catch (...)
{
// there should be no exception
CPPUNIT_ASSERT(false);
}
CPPUNIT_ASSERT(CCopasiMessage::size() == 0);
const SBMLDocument* pDocument = pCOPASIDATAMODEL->getCurrentSBMLDocument();
CPPUNIT_ASSERT(pDocument != NULL);
CPPUNIT_ASSERT(pDocument->getLevel() == 2);
CPPUNIT_ASSERT(pDocument->getVersion() == 3);
const Model* pModel = pDocument->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->getListOfFunctionDefinitions()->size() == 0);
CPPUNIT_ASSERT(pModel->getListOfCompartments()->size() == 1);
CPPUNIT_ASSERT(pModel->getListOfSpecies()->size() == 3);
CPPUNIT_ASSERT(pModel->getListOfReactions()->size() == 1);
CPPUNIT_ASSERT(pModel->getListOfRules()->size() == 1);
const Reaction* pReaction = pModel->getReaction(0);
CPPUNIT_ASSERT(pReaction != NULL);
std::string reactionId = pReaction->getId();
CPPUNIT_ASSERT(reactionId.empty() == false);
const Rule* pRule = pModel->getRule(0);
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pRule->getTypeCode() == SBML_ASSIGNMENT_RULE);
const AssignmentRule* pAssignmentRule = dynamic_cast<const AssignmentRule*>(pRule);
CPPUNIT_ASSERT(pAssignmentRule != NULL);
const Species* pSpecies = pModel->getSpecies(pAssignmentRule->getVariable());
CPPUNIT_ASSERT(pSpecies != NULL);
CPPUNIT_ASSERT(pSpecies->getName() == "C");
const ASTNode* pMath = pAssignmentRule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
CPPUNIT_ASSERT(pMath->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getName() == reactionId);
}
void test000087::test_export_reaction_flux_reference_2()
{
try
{
std::istringstream iss(test000087::MODEL_STRING4);
bool result = load_cps_model_from_stream(iss, *pCOPASIDATAMODEL);
CPPUNIT_ASSERT(result == true);
CPPUNIT_ASSERT(pCOPASIDATAMODEL->getModel() != NULL);
}
catch (...)
{
// there should be no exception
CPPUNIT_ASSERT(false);
}
try
{
std::string result = pCOPASIDATAMODEL->exportSBMLToString(NULL, 2, 1);
CPPUNIT_ASSERT(result.empty());
}
catch (...)
{
// there should be an exception
// check if the correct error message has been created
CPPUNIT_ASSERT(pCOPASIDATAMODEL->getCurrentSBMLDocument() == NULL);
// last message should be an exception
CCopasiMessage message = CCopasiMessage::getLastMessage();
CPPUNIT_ASSERT(message.getType() == CCopasiMessage::EXCEPTION);
// see if the incompatibility message is there
bool found = false;
while (CCopasiMessage::size() > 0)
{
message = CCopasiMessage::getLastMessage();
if (message.getType() == CCopasiMessage::RAW)
{
std::string s = message.getText();
if (s.find(std::string("SBML Incompatibility (10)")) != std::string::npos)
{
found = true;
break;
}
}
}
CPPUNIT_ASSERT_MESSAGE("Error message not found.", found == true);
return;
}
CPPUNIT_ASSERT(false);
}
void test000061::test_bug_1044()
{
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
std::istringstream iss(test000061::MODEL_STRING1);
CPPUNIT_ASSERT(load_cps_model_from_stream(iss, *pDataModel) == true);
CModel* pModel = pDataModel->getModel();
CPPUNIT_ASSERT(pModel != NULL);
// check if the model has been loaded correctly
CPPUNIT_ASSERT(pModel->getModelValues().size() == 1);
const CModelValue* pModelValue = pModel->getModelValues()[0];
CPPUNIT_ASSERT(pModelValue != NULL);
CPPUNIT_ASSERT(pModelValue->getObjectName() == "A");
CPPUNIT_ASSERT(pModelValue->getStatus() == CModelEntity::ASSIGNMENT);
CPPUNIT_ASSERT(pModelValue->getExpressionPtr() != NULL);
const CEvaluationNode* pRoot = pModelValue->getExpressionPtr()->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
CPPUNIT_ASSERT(CEvaluationNode::type(pRoot->getType()) == CEvaluationNode::INVALID);
const SBMLDocument* pDocument = pDataModel->getCurrentSBMLDocument();
CPPUNIT_ASSERT(pDocument == NULL);
// export the model to SBML
bool exception = false;
try
{
CPPUNIT_ASSERT(pDataModel->exportSBMLToString(NULL, 2, 1).empty() == true);
}
catch (...)
{
exception = true;
}
CPPUNIT_ASSERT(exception == true);
CPPUNIT_ASSERT(pDataModel->getCurrentSBMLDocument() == NULL);
// check if the correct error message has been created.
const CCopasiMessage& message = CCopasiMessage::getLastMessage();
CPPUNIT_ASSERT(message.getNumber() == MCSBML + 70);
CPPUNIT_ASSERT(message.getType() == CCopasiMessage::EXCEPTION);
CPPUNIT_ASSERT(CCopasiMessage::size() == 0);
}
void test_compare_utilities::test_copasi_function_expansion()
{
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;;
std::istringstream iss(test_compare_utilities::MODEL_STRING1);
CPPUNIT_ASSERT(load_cps_model_from_stream(iss, *pDataModel) == true);
CFunctionDB* pFunctionDB = CCopasiRootContainer::getFunctionList();
// function_5
CEvaluationTree* pTree = pFunctionDB->findFunction("function_4");
CPPUNIT_ASSERT(pTree != NULL);
// generate a call node
CFunction* pFunction = dynamic_cast<CFunction*>(pTree);
CPPUNIT_ASSERT(pFunction != NULL);
CEvaluationNodeCall* pCallNode = new CEvaluationNodeCall(CEvaluationNode::S_FUNCTION, pFunction->getObjectName());
CPPUNIT_ASSERT(pCallNode != NULL);
CFunctionParameters* pFunctionParameters = &pFunction->getVariables();
unsigned int i = 0, iMax = pFunctionParameters->size();
while (i < iMax)
{
CFunctionParameter* pParameter = (*pFunctionParameters)[i];
CPPUNIT_ASSERT(pParameter != NULL);
CEvaluationNodeVariable* pVariableNode = new CEvaluationNodeVariable(CEvaluationNode::S_DEFAULT, pParameter->getObjectName());
pCallNode->addChild(pVariableNode);
++i;
}
CEvaluationNode* pExpanded = expand_function_calls(pCallNode, pFunctionDB);
delete pCallNode;
CPPUNIT_ASSERT(pExpanded != NULL);
CPPUNIT_ASSERT(pExpanded->mainType() == CEvaluationNode::T_OPERATOR);
CPPUNIT_ASSERT(pExpanded->subType() == CEvaluationNode::S_DIVIDE);
CEvaluationNode* pChild = dynamic_cast<CEvaluationNode*>(pExpanded->getChild());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_OPERATOR);
CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_PLUS);
pChild = dynamic_cast<CEvaluationNode*>(pChild->getChild());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_VARIABLE);
CPPUNIT_ASSERT(pChild->getData() == std::string("y"));
pChild = dynamic_cast<CEvaluationNode*>(pChild->getSibling());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_VARIABLE);
CPPUNIT_ASSERT(pChild->getData() == std::string("x"));
CPPUNIT_ASSERT(pChild->getSibling() == NULL);
pChild = dynamic_cast<CEvaluationNode*>(pExpanded->getChild()->getSibling());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_DOUBLE);
CPPUNIT_ASSERT((fabs(pChild->getValue() - 2.0) / 2.0) < 1e-6);
CPPUNIT_ASSERT(pChild->getSibling() == NULL);
delete pExpanded;
// function_5
pTree = pFunctionDB->findFunction("function_5");
CPPUNIT_ASSERT(pTree != NULL);
// generate a call node
pFunction = dynamic_cast<CFunction*>(pTree);
CPPUNIT_ASSERT(pFunction != NULL);
pCallNode = new CEvaluationNodeCall(CEvaluationNode::S_FUNCTION, pFunction->getObjectName());
CPPUNIT_ASSERT(pCallNode != NULL);
pFunctionParameters = &pFunction->getVariables();
i = 0, iMax = pFunctionParameters->size();
while (i < iMax)
{
CFunctionParameter* pParameter = (*pFunctionParameters)[i];
CPPUNIT_ASSERT(pParameter != NULL);
CEvaluationNodeVariable* pVariableNode = new CEvaluationNodeVariable(CEvaluationNode::S_DEFAULT, pParameter->getObjectName());
pCallNode->addChild(pVariableNode);
++i;
}
pExpanded = expand_function_calls(pCallNode, pFunctionDB);
delete pCallNode;
CPPUNIT_ASSERT(pExpanded != NULL);
CPPUNIT_ASSERT(pExpanded->mainType() == CEvaluationNode::T_OPERATOR);
CPPUNIT_ASSERT(pExpanded->subType() == CEvaluationNode::S_PLUS);
pChild = dynamic_cast<CEvaluationNode*>(pExpanded->getChild());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_OPERATOR);
CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_MINUS);
pChild = dynamic_cast<CEvaluationNode*>(pChild->getChild());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_VARIABLE);
CPPUNIT_ASSERT(pChild->getData() == std::string("a"));
pChild = dynamic_cast<CEvaluationNode*>(pChild->getSibling());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_OPERATOR);
CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_MULTIPLY);
CPPUNIT_ASSERT(pChild->getSibling() == NULL);
pChild = dynamic_cast<CEvaluationNode*>(pChild->getChild());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_VARIABLE);
CPPUNIT_ASSERT(pChild->getData() == std::string("c"));
pChild = dynamic_cast<CEvaluationNode*>(pChild->getSibling());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_DOUBLE);
CPPUNIT_ASSERT((fabs(pChild->getValue() - 1.3) / 1.3) < 1e-6);
CPPUNIT_ASSERT(pChild->getSibling() == NULL);
// (3*b)-5.23
pChild = dynamic_cast<CEvaluationNode*>(pExpanded->getChild()->getSibling());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_OPERATOR);
CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_MINUS);
// 3*b
pChild = dynamic_cast<CEvaluationNode*>(pChild->getChild());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_OPERATOR);
CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_MULTIPLY);
pChild = dynamic_cast<CEvaluationNode*>(pChild->getChild());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_DOUBLE);
CPPUNIT_ASSERT((fabs(pChild->getValue() - 3.0) / 3.0) < 1e-6);
pChild = dynamic_cast<CEvaluationNode*>(pChild->getSibling());
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_VARIABLE);
CPPUNIT_ASSERT(pChild->getData() == std::string("b"));
CPPUNIT_ASSERT(pChild->getSibling() == NULL);
// 5.23
pChild = dynamic_cast<CEvaluationNode*>(pExpanded->getChild()->getSibling()->getChild()->getSibling());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_DOUBLE);
CPPUNIT_ASSERT((fabs(pChild->getValue() - 5.23) / 5.23) < 1e-6);
CPPUNIT_ASSERT(pChild->getSibling() == NULL);
delete pExpanded;
// function_6
pTree = pFunctionDB->findFunction("function_6");
CPPUNIT_ASSERT(pTree != NULL);
// generate a call node
pFunction = dynamic_cast<CFunction*>(pTree);
CPPUNIT_ASSERT(pFunction != NULL);
pCallNode = new CEvaluationNodeCall(CEvaluationNode::S_FUNCTION, pFunction->getObjectName());
CPPUNIT_ASSERT(pCallNode != NULL);
pFunctionParameters = &pFunction->getVariables();
i = 0, iMax = pFunctionParameters->size();
while (i < iMax)
{
CFunctionParameter* pParameter = (*pFunctionParameters)[i];
CPPUNIT_ASSERT(pParameter != NULL);
CEvaluationNodeVariable* pVariableNode = new CEvaluationNodeVariable(CEvaluationNode::S_DEFAULT, pParameter->getObjectName());
pCallNode->addChild(pVariableNode);
++i;
}
pExpanded = expand_function_calls(pCallNode, pFunctionDB);
delete pCallNode;
CPPUNIT_ASSERT(pExpanded != NULL);
// (k1-k3*1.3)+((3*k2)-5.23)
CPPUNIT_ASSERT(pExpanded->mainType() == CEvaluationNode::T_OPERATOR);
CPPUNIT_ASSERT(pExpanded->subType() == CEvaluationNode::S_PLUS);
pChild = dynamic_cast<CEvaluationNode*>(pExpanded->getChild());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_OPERATOR);
CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_MINUS);
pChild = dynamic_cast<CEvaluationNode*>(pChild->getChild());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_VARIABLE);
CPPUNIT_ASSERT(pChild->getData() == std::string("k1"));
pChild = dynamic_cast<CEvaluationNode*>(pChild->getSibling());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_OPERATOR);
CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_MULTIPLY);
CPPUNIT_ASSERT(pChild->getSibling() == NULL);
pChild = dynamic_cast<CEvaluationNode*>(pChild->getChild());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_VARIABLE);
CPPUNIT_ASSERT(pChild->getData() == std::string("k3"));
pChild = dynamic_cast<CEvaluationNode*>(pChild->getSibling());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_DOUBLE);
CPPUNIT_ASSERT((fabs(pChild->getValue() - 1.3) / 1.3) < 1e-6);
CPPUNIT_ASSERT(pChild->getSibling() == NULL);
// (3*b)-5.23
pChild = dynamic_cast<CEvaluationNode*>(pExpanded->getChild()->getSibling());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_OPERATOR);
CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_MINUS);
// 3*b
pChild = dynamic_cast<CEvaluationNode*>(pChild->getChild());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_OPERATOR);
CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_MULTIPLY);
pChild = dynamic_cast<CEvaluationNode*>(pChild->getChild());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_DOUBLE);
CPPUNIT_ASSERT((fabs(pChild->getValue() - 3.0) / 3.0) < 1e-6);
pChild = dynamic_cast<CEvaluationNode*>(pChild->getSibling());
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_VARIABLE);
CPPUNIT_ASSERT(pChild->getData() == std::string("k2"));
CPPUNIT_ASSERT(pChild->getSibling() == NULL);
// 5.23
pChild = dynamic_cast<CEvaluationNode*>(pExpanded->getChild()->getSibling()->getChild()->getSibling());
CPPUNIT_ASSERT(pChild != NULL);
CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_DOUBLE);
CPPUNIT_ASSERT((fabs(pChild->getValue() - 5.23) / 5.23) < 1e-6);
CPPUNIT_ASSERT(pChild->getSibling() == NULL);
delete pExpanded;
}
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());
}
// tests whether we are importing global render information
void test000098::test_export_notes()
{
CPPUNIT_ASSERT(pDataModel != NULL);
std::istringstream iss(test000098::CPS_MODEL_1);
CPPUNIT_ASSERT(load_cps_model_from_stream(iss, *pDataModel) == true);
std::string s;
try
{
s = pDataModel->exportSBMLToString(NULL, 2, 1);
}
catch (...)
{
CPPUNIT_ASSERT(false);
}
CPPUNIT_ASSERT(!s.empty());
SBMLReader reader;
SBMLDocument* pSBMLDocument = NULL;
try
{
pSBMLDocument = reader.readSBMLFromString(s);
}
catch (...)
{
CPPUNIT_ASSERT(false);
}
CPPUNIT_ASSERT(pSBMLDocument != NULL);
Model* pModel = pSBMLDocument->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->isSetNotes() == true);
std::string notes = pModel->getNotesString();
CPPUNIT_ASSERT(!notes.empty());
CPPUNIT_ASSERT(notes.find("Simple note on model") != std::string::npos);
CPPUNIT_ASSERT(pModel->getNumCompartments() == 1);
CPPUNIT_ASSERT(pModel->getNumSpecies() == 1);
CPPUNIT_ASSERT(pModel->getNumParameters() == 1);
CPPUNIT_ASSERT(pModel->getNumReactions() == 1);
CPPUNIT_ASSERT(pModel->getNumEvents() == 1);
// compartment
SBase* pObject = pModel->getCompartment(0);
CPPUNIT_ASSERT(pObject != NULL);
CPPUNIT_ASSERT(pObject->isSetNotes() == true);
notes = pObject->getNotesString();
CPPUNIT_ASSERT(!notes.empty());
CPPUNIT_ASSERT(notes.find("Simple note on compartment") != std::string::npos);
// species
pObject = pModel->getSpecies(0);
CPPUNIT_ASSERT(pObject != NULL);
CPPUNIT_ASSERT(pObject->isSetNotes() == true);
notes = pObject->getNotesString();
CPPUNIT_ASSERT(!notes.empty());
CPPUNIT_ASSERT(notes.find("Simple note on species") != std::string::npos);
// parameter
pObject = pModel->getParameter(0);
CPPUNIT_ASSERT(pObject != NULL);
CPPUNIT_ASSERT(pObject->isSetNotes() == true);
notes = pObject->getNotesString();
CPPUNIT_ASSERT(!notes.empty());
CPPUNIT_ASSERT(notes.find("Simple note on parameter") != std::string::npos);
// reaction
pObject = pModel->getReaction(0);
CPPUNIT_ASSERT(pObject != NULL);
CPPUNIT_ASSERT(pObject->isSetNotes() == true);
notes = pObject->getNotesString();
CPPUNIT_ASSERT(!notes.empty());
CPPUNIT_ASSERT(notes.find("Simple note on reaction") != std::string::npos);
// event
pObject = pModel->getEvent(0);
CPPUNIT_ASSERT(pObject != NULL);
CPPUNIT_ASSERT(pObject->isSetNotes() == true);
notes = pObject->getNotesString();
CPPUNIT_ASSERT(!notes.empty());
CPPUNIT_ASSERT(notes.find("Simple note on event") != std::string::npos);
}
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);
}