void checkReactions(Model* model, set<string>& components, set<string>& tests, const map<string, vector<double> >& results, int type)
{
if (model->getNumReactions() > 0) {
components.insert("Reaction");
for (unsigned int r=0; r<model->getNumReactions(); r++) {
Reaction* rxn = model->getReaction(r);
if (rxn->isSetFast() && rxn->getFast()) {
tests.insert("FastReaction");
}
if (rxn->isSetReversible() && rxn->getReversible()) {
if (type!=1) {
tests.insert("ReversibleReaction [?]");
}
}
ListOfSpeciesReferences* reactants = rxn->getListOfReactants();
checkSpeciesRefs(model, reactants, components, tests, results);
ListOfSpeciesReferences* products = rxn->getListOfProducts();
checkSpeciesRefs(model, products, components, tests, results);
if (rxn->isSetKineticLaw()) {
KineticLaw* kl = rxn->getKineticLaw();
if (kl->getNumParameters() > 0) {
tests.insert("LocalParameters");
}
if (kl->isSetMath() == false) {
tests.insert("NoMathML");
}
}
}
}
}
/* adds species referred to in a KineticLaw to the ListOfModifiers
* this will only be applicable when up converting an L1 model
*/
void
Model::addModifiers ()
{
//
// Level 2/3 has a listOfModifiers associated with a Reaction
// which are not listed in a L1 Model.
// For each symbol in the Reaction's KineticLaw,
// that symbol is a modifier iff:
//
// 1. It is defined as a Species in the Model
// 2. It is not a Reactant or Product in this Reaction.
//
// Thus modifiers must be added where appropriate.
//
const char *id;
unsigned int size;
unsigned int n, l;
const ASTNode *node;
List *names;
KineticLaw* kl;
for (n = 0; n < getNumReactions(); n++)
{
kl = getReaction(n)->getKineticLaw();
if (kl == NULL || kl->isSetMath() == false) continue;
node = kl->getMath();
names = node->getListOfNodes((ASTNodePredicate) ASTNode_isName);
size = names->getSize();
for (l = 0; l < size; l++)
{
node = (ASTNode *) names->get(l);
id = node->getName();
// 1. It is an AST_NAME (not AST_NAME_TIME), and
if (node->getType() != AST_NAME) continue;
// 2. It refers to a Species in this Model, and
if (id == NULL || getSpecies(id) == NULL) continue;
// 3. It is not a Reactant, Product, or (already) a Modifier
if (getReaction(n)->getReactant(id) != NULL) continue;
if (getReaction(n)->getProduct (id) != NULL) continue;
if (getReaction(n)->getModifier(id) != NULL) continue;
getReaction(n)->createModifier()->setSpecies(id);
}
delete names;
}
}
/** @cond doxygenLibsbmlInternal */
int
Replacing::updateIDs(SBase* oldnames, SBase* newnames)
{
int ret = LIBSBML_OPERATION_SUCCESS;
SBMLDocument* doc = getSBMLDocument();
if (oldnames->isSetId() && !newnames->isSetId()) {
if (doc) {
string error = "Unable to transform IDs in Replacing::updateIDs during replacement: the '" + oldnames->getId() + "' element's replacement does not have an ID set.";
doc->getErrorLog()->logPackageError("comp", CompMustReplaceIDs, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_INVALID_OBJECT;
}
if (oldnames->isSetMetaId() && !newnames->isSetMetaId()) {
if (doc) {
string error = "Unable to transform IDs in Replacing::updateIDs during replacement: the replacement of the element with metaid '" + oldnames->getMetaId() + "' does not have a metaid.";
doc->getErrorLog()->logPackageError("comp", CompMustReplaceMetaIDs, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_INVALID_OBJECT;
}
//LS DEBUG Somehow we need to check identifiers from other packages here (like spatial id's). How, exactly, is anyone's guess.
Model* replacedmod = const_cast<Model*>(CompBase::getParentModel(oldnames));
KineticLaw* replacedkl;
ASTNode newkl;
if (replacedmod==NULL) {
if (doc) {
string error = "Unable to transform IDs in Replacing::updateIDs during replacement: the replacement of '" + oldnames->getId() + "' does not have a valid model.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_INVALID_OBJECT;
}
List* allElements = replacedmod->getAllElements();
string oldid = oldnames->getId();
string newid = newnames->getId();
if (!oldid.empty()) {
switch(oldnames->getTypeCode()) {
case SBML_UNIT_DEFINITION:
replacedmod->renameUnitSIdRefs(oldid, newid);
for (unsigned int e=0; e<allElements->getSize(); e++) {
SBase* element = static_cast<SBase*>(allElements->get(e));
element->renameUnitSIdRefs(oldid, newid);
}
break;
case SBML_LOCAL_PARAMETER:
replacedkl = static_cast<KineticLaw*>(oldnames->getAncestorOfType(SBML_KINETIC_LAW));
if (replacedkl->isSetMath()) {
newkl = *replacedkl->getMath();
newkl.renameSIdRefs(oldid, newid);
replacedkl->setMath(&newkl);
}
break;
case SBML_COMP_PORT:
break;
//LS DEBUG And here is where we would need some sort of way to check if the id wasn't an SId for some objects.
default:
replacedmod->renameSIdRefs(oldnames->getId(), newnames->getId());
for (unsigned int e=0; e<allElements->getSize(); e++) {
SBase* element = static_cast<SBase*>(allElements->get(e));
element->renameSIdRefs(oldid, newid);
}
}
}
string oldmetaid = oldnames->getMetaId();
string newmetaid = newnames->getMetaId();
if (oldnames->isSetMetaId()) {
replacedmod->renameMetaIdRefs(oldmetaid, newmetaid);
for (unsigned int e=0; e<allElements->getSize(); e++) {
SBase* element = static_cast<SBase*>(allElements->get(e));
element->renameMetaIdRefs(oldmetaid, newmetaid);
}
}
//LS DEBUG And here is where we would need some sort of way to check for ids that were not 'id' or 'metaid'.
delete allElements;
return ret;
}
int Submodel::convertTimeAndExtentWith(const ASTNode* tcf, const ASTNode* xcf, const ASTNode* klmod)
{
if (tcf==NULL && xcf==NULL) return LIBSBML_OPERATION_SUCCESS;
Model* model = getInstantiation();
if (model==NULL) {
//getInstantiation sets its own error messages.
return LIBSBML_OPERATION_FAILED;
}
ASTNode tcftimes(AST_TIMES);
ASTNode tcfdiv(AST_DIVIDE);
if (tcf != NULL) {
tcftimes.addChild(tcf->deepCopy());
tcfdiv.addChild(tcf->deepCopy());
}
ASTNode rxndivide(AST_DIVIDE);
if (klmod != NULL) {
ASTNode rxnref(AST_NAME);
rxndivide.addChild(rxnref.deepCopy());
rxndivide.addChild(klmod->deepCopy());
}
List* allElements = model->getAllElements();
for (ListIterator iter = allElements->begin(); iter != allElements->end(); ++iter)
{
SBase* element = static_cast<SBase*>(*iter);
assert(element != NULL);
ASTNode* ast1 = NULL;
ASTNode* ast2 = NULL;
Constraint* constraint = NULL;
Delay* delay = NULL;
EventAssignment* ea = NULL;
InitialAssignment* ia = NULL;
KineticLaw* kl = NULL;
Priority* priority = NULL;
RateRule* rrule = NULL;
Rule* rule = NULL;
Submodel* submodel = NULL;
Trigger* trigger = NULL;
string cf = "";
//Reaction math will be converted below, in the bits with the kinetic law. But because of that, we need to handle references *to* the reaction: even if it has no kinetic law, the units have changed, and this needs to be reflected by the flattening routine.
if (rxndivide.getNumChildren() != 0 && element->getTypeCode()==SBML_REACTION && element->isSetId()) {
rxndivide.getChild(0)->setName(element->getId().c_str());
for (ListIterator iter = allElements->begin(); iter != allElements->end(); ++iter)
{
SBase* subelement = static_cast<SBase*>(*iter);
subelement->replaceSIDWithFunction(element->getId(), &rxndivide);
}
}
//Submodels need their timeConversionFactor and extentConversionFactor attributes converted. We're moving top-down, so all we need to do here is fix the conversion factor attributes themselves, pointing them to new parameters if need be.
if ((tcf !=NULL || xcf != NULL) && element->getTypeCode()==SBML_COMP_SUBMODEL) {
submodel = static_cast<Submodel*>(element);
if (tcf != NULL) {
if (submodel->isSetTimeConversionFactor()) {
createNewConversionFactor(cf, tcf, submodel->getTimeConversionFactor(), model);
submodel->setTimeConversionFactor(cf);
}
else {
submodel->setTimeConversionFactor(tcf->getName());
}
}
if (xcf != NULL) {
if (submodel->isSetExtentConversionFactor()) {
createNewConversionFactor(cf, xcf, submodel->getExtentConversionFactor(), model);
submodel->setExtentConversionFactor(cf);
}
else {
submodel->setExtentConversionFactor(xcf->getName());
}
}
}
if (tcf==NULL) {
if (klmod !=NULL && element->getTypeCode()==SBML_KINETIC_LAW) {
kl = static_cast<KineticLaw*>(element);
if (kl->isSetMath()) {
ast1 = new ASTNode(AST_TIMES);
ast1->addChild(klmod->deepCopy());
ast1->addChild(kl->getMath()->deepCopy());
kl->setMath(ast1);
delete ast1;
}
}
}
else {
// All math 'time' and 'delay' csymbols must still be converted.
// Also, several constructs are modified directly.
switch(element->getTypeCode()) {
//This would be a WHOLE LOT SIMPLER if there was a 'hasMath' class in libsbml. But even so, it would have to
// handle the kinetic laws, rate rules, and delays separately.
case SBML_KINETIC_LAW:
//Kinetic laws are multiplied by 'klmod'.
kl = static_cast<KineticLaw*>(element);
ast1 = kl->getMath()->deepCopy();
convertCSymbols(ast1, &tcfdiv, &tcftimes);
if (klmod !=NULL) {
kl = static_cast<KineticLaw*>(element);
if (kl->isSetMath()) {
ast2 = new ASTNode(AST_TIMES);
ast2->addChild(klmod->deepCopy());
ast2->addChild(ast1);
kl->setMath(ast2);
delete ast2;
}
}
else {
kl->setMath(ast1);
delete ast1;
}
break;
case SBML_DELAY:
//Delays are multiplied by the time conversion factor.
delay = static_cast<Delay*>(element);
if (delay->isSetMath()) {
ast1 = delay->getMath()->deepCopy();
convertCSymbols(ast1, &tcfdiv, &tcftimes);
tcftimes.addChild(ast1);
delay->setMath(&tcftimes);
tcftimes.removeChild(1);
delete ast1;
}
break;
case SBML_RATE_RULE:
//Rate rules are divided by the time conversion factor.
rrule = static_cast<RateRule*>(element);
if (rrule->isSetMath()) {
ast1 = rrule->getMath()->deepCopy();
tcfdiv.insertChild(0, ast1);
rrule->setMath(&tcfdiv);
tcfdiv.removeChild(0);
delete ast1;
}
//Fall through to:
case SBML_ASSIGNMENT_RULE:
case SBML_ALGEBRAIC_RULE:
//Rules in general need csymbols converted.
rule = static_cast<Rule*>(element);
if (rule->isSetMath()) {
ast1 = rule->getMath()->deepCopy();
convertCSymbols(ast1, &tcfdiv, &tcftimes);
rule->setMath(ast1);
delete ast1;
}
break;
case SBML_EVENT_ASSIGNMENT:
//Event assignments need csymbols converted.
ea = static_cast<EventAssignment*>(element);
if (ea->isSetMath()) {
ast1 = ea->getMath()->deepCopy();
convertCSymbols(ast1, &tcfdiv, &tcftimes);
ea->setMath(ast1);
delete ast1;
}
break;
case SBML_INITIAL_ASSIGNMENT:
//Initial assignments need csymbols converted.
ia = static_cast<InitialAssignment*>(element);
if (ia->isSetMath()) {
ast1 = ia->getMath()->deepCopy();
convertCSymbols(ast1, &tcfdiv, &tcftimes);
ia->setMath(ast1);
delete ast1;
}
break;
case SBML_CONSTRAINT:
//Constraints need csymbols converted.
constraint = static_cast<Constraint*>(element);
if (constraint->isSetMath()) {
ast1 = constraint->getMath()->deepCopy();
convertCSymbols(ast1, &tcfdiv, &tcftimes);
constraint->setMath(ast1);
delete ast1;
}
break;
case SBML_PRIORITY:
//Priorities need csymbols converted.
priority = static_cast<Priority*>(element);
if (priority->isSetMath()) {
ast1 = priority->getMath()->deepCopy();
convertCSymbols(ast1, &tcfdiv, &tcftimes);
priority->setMath(ast1);
delete ast1;
}
break;
case SBML_TRIGGER:
//Triggers need csymbols converted.
trigger = static_cast<Trigger*>(element);
if (trigger->isSetMath()) {
ast1 = trigger->getMath()->deepCopy();
convertCSymbols(ast1, &tcfdiv, &tcftimes);
trigger->setMath(ast1);
delete ast1;
}
break;
default:
//Do nothing! If we wanted to call a plugin routine, this would be the place. The only other alternative is to #ifdef some code in here that deals with the math-containing package objects explicitly. Which might be the best option, all told.
break;
}
}
}
delete allElements;
return LIBSBML_OPERATION_SUCCESS;
}
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());
}