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);
}
/**
* This method tries to import CellDesigner annotations.
*/
void DataModelGUI::importCellDesigner()
{
// add code to check for CellDesigner annotations
// ask the user if the annotations should be imported
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
if (pDataModel != NULL)
{
SBMLDocument* pSBMLDocument = pDataModel->getCurrentSBMLDocument();
if (pSBMLDocument != NULL &&
pSBMLDocument->getModel() != NULL &&
pSBMLDocument->getModel()->getAnnotation() != NULL)
{
// check for the CellDesigner namespace
std::pair<bool, std::string> foundNamespace = CCellDesignerImporter::findCellDesignerNamespace(pSBMLDocument);
if (foundNamespace.first == true)
{
const XMLNode* pAnno = CCellDesignerImporter::findCellDesignerAnnotation(pSBMLDocument, pSBMLDocument->getModel()->getAnnotation());
// first we check if there are supported cell designer annotations
if (pAnno != NULL)
{
// check if the file contains the correct version
double version = CCellDesignerImporter::determineVersion(pAnno);
if (version < 4.0)
{
CCopasiMessage(CCopasiMessage::RAW, "CellDesigner annotation was found in the file, but the version is not supported.\nPlease open the file in the latest version of CellDesigner and save it again.");
}
else
{
bool importCD = false;
#if LIBSBML_VERSION >= 50400
// if we don't have a layout import it!
LayoutModelPlugin* mplugin = (LayoutModelPlugin*)pSBMLDocument->getModel()->getPlugin("layout");
if (mplugin == NULL || (mplugin != NULL && mplugin->getNumLayouts() == 0))
importCD = true;
#endif
// ask the user if the CellDesigner annotation should be imported
if (importCD || CQMessageBox::question(NULL, "CellDesigner import", "A CellDesigner diagram was found in this file.\nDo you want to import the diagram?" , QMessageBox::Yes | QMessageBox::No , QMessageBox::No) == QMessageBox::Yes)
{
// do the import
CCellDesignerImporter cd_importer(pSBMLDocument);
if (cd_importer.getLayout() == NULL)
{
CCopasiMessage(CCopasiMessage::WARNING, "Sorry, CellDesigner annotations could not be importet.");
}
else
{
// now we have to import the created layout
// create the model map
std::string s1, s2;
std::map<std::string, std::string> modelmap;
std::map<CCopasiObject*, SBase*>::const_iterator it;
std::map<CCopasiObject*, SBase*>::const_iterator itEnd = pDataModel->getCopasi2SBMLMap().end();
for (it = pDataModel->getCopasi2SBMLMap().begin(); it != itEnd; ++it)
{
s1 = SBMLUtils::getIdFromSBase(it->second);
if (it->first)
{
s2 = it->first->getKey();
}
else
{
s2 = "";
}
if ((s1 != "") && (s2 != ""))
{
modelmap[s1] = s2;
}
}
// the layout map and the id to key map can be empty
std::map<std::string, std::string> layoutmap;
std::map<std::string, std::string> idToKeyMap;
#ifdef USE_CRENDER_EXTENSION
CLayout* pLayout = SBMLDocumentLoader::createLayout(*cd_importer.getLayout(), modelmap, layoutmap, idToKeyMap);
#else
CLayout* pLayout = SBMLDocumentLoader::createLayout(*cd_importer.getLayout(), modelmap, layoutmap);
#endif /* USE_CRENDER_EXTENSION */
// add the layout to the DataModel
if (pLayout != NULL && pDataModel->getListOfLayouts() != NULL)
{
// the addLayout methods expects a map as the second argument which currently is
// ignored, so we just pass an empty one
// TODO maybe the methods actually expects one of the maps above (layoutmap or idToKeyMap), but
// TODO this is not documented in CListOfLayouts
std::map<std::string, std::string> tmp;
pDataModel->getListOfLayouts()->addLayout(pLayout, tmp);
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, "Sorry, Layout from CellDesigner annotations could not be created.");
}
}
}
}
}
else
{
CCopasiMessage(CCopasiMessage::RAW, "CellDesigner annotation was found in the file, but the version is not supported.\nPlease open the file in the latest version of CellDesigner and save it again.");
}
}
}
}
}
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);
}
