//Deprecated function
int Replacing::performReplacement()
{
set<SBase*> toremove;
set<SBase*>* removed = NULL;
CompModelPlugin* cmp = NULL;
SBase* parent = getParentSBMLObject();
while (parent != NULL && parent->getTypeCode() != SBML_DOCUMENT) {
if (parent->getTypeCode() == SBML_COMP_MODELDEFINITION ||
parent->getTypeCode() == SBML_MODEL) {
cmp = static_cast<CompModelPlugin*>(parent->getPlugin("comp"));
if (cmp != NULL) {
removed = cmp->getRemovedSet();
}
}
parent = parent->getParentSBMLObject();
}
int ret = performReplacementAndCollect(removed, &toremove);
if (ret != LIBSBML_OPERATION_SUCCESS) {
return ret;
}
if (cmp == NULL) {
return LIBSBML_INVALID_OBJECT;
}
return cmp->removeCollectedElements(removed, &toremove);
}
/*
* Constructs and returns a UnitDefinition that expresses the units of this
* Parameter.
*/
UnitDefinition *
Parameter::getDerivedUnitDefinition()
{
/* if we have the whole model but it is not in a document
* it is still possible to determine the units
*/
Model * m = static_cast <Model *> (getAncestorOfType(SBML_MODEL));
if (m != NULL)
{
if (!m->isPopulatedListFormulaUnitsData())
{
m->populateListFormulaUnitsData();
}
/* need to distinguish between a global and local parameter
* for a global parameter a unit definition will have been created
* for a local parameter need to create one based on the units field
*/
bool globalParameter = false;
SBase *parent = getParentSBMLObject();
SBase *pparent = (parent) ? parent->getParentSBMLObject() : NULL;
if (pparent != NULL && dynamic_cast<Model*>(pparent) != 0)
globalParameter = true;
if (globalParameter)
{
if (m->getFormulaUnitsData(getId(), getTypeCode()) != NULL)
{
return m->getFormulaUnitsData(getId(), getTypeCode())
->getUnitDefinition();
}
else
{
return NULL;
}
}
else
{
UnitDefinition *ud = NULL;
const char * units = getUnits().c_str();
if (!strcmp(units, ""))
{
ud = new UnitDefinition(getSBMLNamespaces());
return ud;
}
else
{
if (UnitKind_isValidUnitKindString(units,
getLevel(), getVersion()))
{
Unit * unit = new Unit(getSBMLNamespaces());
unit->setKind(UnitKind_forName(units));
unit->initDefaults();
ud = new UnitDefinition(getSBMLNamespaces());
ud->addUnit(unit);
delete unit;
}
else
{
/* must be a unit definition */
ud = static_cast <Model *> (getAncestorOfType(SBML_MODEL))->getUnitDefinition(units);
}
return ud;
}
}
}
else
{
return NULL;
}
}
int
Submodel::instantiate()
{
SBMLDocument* doc = getSBMLDocument();
SBMLDocument* rootdoc = doc;
if (doc==NULL)
{
return LIBSBML_OPERATION_FAILED;
}
CompSBMLDocumentPlugin* docplugin =
static_cast<CompSBMLDocumentPlugin*>(doc->getPlugin(getPrefix()));
if (docplugin==NULL)
{
return LIBSBML_OPERATION_FAILED;
}
SBase* parent = getParentSBMLObject();
string parentmodelname = "";
string parentURI = "";
set<string> uniqueModels;
while (parent != NULL && parent->getTypeCode() != SBML_DOCUMENT) {
if (parent->getTypeCode() == SBML_COMP_SUBMODEL) {
const Submodel* parentsub = static_cast<const Submodel*>(parent);
uniqueModels.insert(parentsub->mInstantiationOriginalURI + "::" + parentsub->getModelRef());
if (parentURI=="") {
parentURI=parentsub->mInstantiationOriginalURI;
}
}
if (parent->getTypeCode() == SBML_MODEL ||
parent->getTypeCode() == SBML_COMP_MODELDEFINITION)
{
if (parentmodelname == "") {
parentmodelname = parent->getId();
}
}
rootdoc = parent->getSBMLDocument();
parent = parent->getParentSBMLObject();
}
if (mInstantiatedModel != NULL)
{
delete mInstantiatedModel;
mInstantiatedModel = NULL;
mInstantiationOriginalURI.clear();
}
if (!hasRequiredAttributes()) {
string error = "Instantiation error in Submodel::instantiate: ";
if (!isSetId()) {
error += "A submodel in model '" + getParentModel(this)->getId() + "' does not have an 'id' attribute.";
}
else if (!isSetModelRef()) {
error += "The submodel '" + getId() + "' does not have a 'modelRef' attribute.";
}
rootdoc->getErrorLog()->logPackageError("comp", CompSubmodelAllowedAttributes, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
return LIBSBML_INVALID_OBJECT;
}
SBase* origmodel = docplugin->getModel(getModelRef());
if (origmodel==NULL) {
string error = "In Submodel::instantiate, unable to instantiate submodel '" + getId() + "' because the referenced model ('" + getModelRef() +"') does not exist.";
rootdoc->getErrorLog()->logPackageError("comp", CompSubmodelMustReferenceModel, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
return LIBSBML_INVALID_OBJECT;
}
ExternalModelDefinition* extmod;
SBMLDocument* origdoc = NULL;
string newmodel = parentURI + "::" + getModelRef();
set<pair<string, string> > parents;
switch(origmodel->getTypeCode())
{
case SBML_MODEL:
case SBML_COMP_MODELDEFINITION:
origdoc = origmodel->getSBMLDocument();
mInstantiatedModel = static_cast<Model*>(origmodel)->clone();
if (uniqueModels.insert(newmodel).second == false) {
//Can't instantiate this model, because we are already a child of it.
string error = "Error in Submodel::instantiate: cannot instantiate submodel '" + getId() + "' in model '" + parentmodelname + "' because it references the model '" + getModelRef() + "', which is already an ancestor of the submodel.";
rootdoc->getErrorLog()->logPackageError("comp", CompSubmodelCannotReferenceSelf, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
return LIBSBML_OPERATION_FAILED;
}
mInstantiationOriginalURI = parentURI;
break;
case SBML_COMP_EXTERNALMODELDEFINITION:
extmod = static_cast<ExternalModelDefinition*>(origmodel);
if (extmod==NULL)
{
//No error message: it should be impossible, if origmodel has the type code 'external model definition', for it to not be castable to an external model definition.
mInstantiatedModel = NULL;
mInstantiationOriginalURI = "";
return LIBSBML_OPERATION_FAILED;
}
mInstantiatedModel = extmod->getReferencedModel(rootdoc, parents);
if (mInstantiatedModel == NULL)
{
string error = "In Submodel::instantiate, unable to instantiate submodel '" + getId() + "' because the external model definition it referenced (model '" + getModelRef() +"') could not be resolved.";
rootdoc->getErrorLog()->logPackageError("comp", CompSubmodelMustReferenceModel, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
mInstantiationOriginalURI = "";
return LIBSBML_OPERATION_FAILED;
}
mInstantiationOriginalURI = extmod->getSource();
origdoc = mInstantiatedModel->getSBMLDocument();
newmodel = extmod->getSource() + "::" + getModelRef();
if (uniqueModels.insert(newmodel).second == false) {
//Can't instantiate this model, because we are already a child of it.
string error = "Error in Submodel::instantiate: cannot instantiate submodel '" + getId() + "' in model '" + parentmodelname + "' because it references the model '" + getModelRef() + "', which is already an ancestor of the submodel.";
rootdoc->getErrorLog()->logPackageError("comp", CompSubmodelCannotReferenceSelf, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
mInstantiatedModel = NULL;
mInstantiationOriginalURI = "";
return LIBSBML_OPERATION_FAILED;
}
mInstantiatedModel = mInstantiatedModel->clone();
mInstantiationOriginalURI = extmod->getSource();
break;
default:
//Should always be one of the above, unless someone extends one of the above and doesn't tell us.
string error = "Instantiation error in Submodel::instantiate: unable to parse the model '" + origmodel->getId() + "', as it was not of the type 'model' 'modelDefinition', or 'externalModelDefinition'. The most likely cause of this situation is if some other package extended one of those three types, but the submodel code was not updated.";
rootdoc->getErrorLog()->logPackageError("comp", CompUnresolvedReference, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
mInstantiatedModel = NULL;
mInstantiationOriginalURI = "";
return LIBSBML_OPERATION_FAILED;
}
if (mInstantiatedModel==NULL)
{
string error = "Instantiation error in Submodel::instantiate: unable to create a valid copy of model '" + getModelRef() + "'.";
rootdoc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
mInstantiationOriginalURI = "";
return LIBSBML_OPERATION_FAILED;
}
mInstantiatedModel->connectToParent(this);
mInstantiatedModel->setSBMLDocument(origdoc);
mInstantiatedModel->enablePackage(getPackageURI(), getPrefix(), true);
CompModelPlugin* instmodplug =
static_cast<CompModelPlugin*>(mInstantiatedModel->getPlugin(getPrefix()));
if (instmodplug == NULL)
{
mInstantiatedModel->enablePackageInternal(getPackageURI(), getPrefix(), true);
}
// call all registered callbacks
std::vector<ModelProcessingCallbackData*>::iterator it = mProcessingCBs.begin();
while(it != mProcessingCBs.end())
{
ModelProcessingCallbackData* current = *it;
int result = current->cb(mInstantiatedModel, rootdoc->getErrorLog(), current->data);
if (result != LIBSBML_OPERATION_SUCCESS)
return result;
++it;
}
CompModelPlugin* origmodplug =
static_cast<CompModelPlugin*>(rootdoc->getModel()->getPlugin(getPrefix()));
instmodplug =
static_cast<CompModelPlugin*>(mInstantiatedModel->getPlugin(getPrefix()));
if (instmodplug == NULL)
return LIBSBML_OPERATION_SUCCESS;
// if we have a transformer specified, then we need to propagate it, so it can
// be used
if (origmodplug->isSetTransformer())
{
if (instmodplug != NULL)
instmodplug->setTransformer(origmodplug->getTransformer());
}
for (unsigned int sub=0; sub<instmodplug->getNumSubmodels(); sub++)
{
Submodel* instsub = instmodplug->getSubmodel(sub);
int ret = instsub->instantiate();
if (ret != LIBSBML_OPERATION_SUCCESS) {
//'instantiate' already sets its own error messages.
delete mInstantiatedModel;
mInstantiatedModel = NULL;
mInstantiationOriginalURI = "";
return ret;
}
}
return LIBSBML_OPERATION_SUCCESS;
}
int ReplacedElement::performReplacementAndCollect(set<SBase*>* removed, set<SBase*>* toremove)
{
SBMLDocument* doc = getSBMLDocument();
if (isSetDeletion()) {
//Deletions don't need to be replaced.
return LIBSBML_OPERATION_SUCCESS;
}
//Find the various objects and plugin objects we need for this to work.
SBase* lore = getParentSBMLObject();
ListOf* lorelist = static_cast<ListOf*>(lore);
if (lore == NULL) {
if (doc) {
string error = "Cannot carry out replacement in ReplacedElement::performReplacement: no parent <listOfReplacedElements> could be found for the given replacement element.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_INVALID_OBJECT;
}
if (lore->getTypeCode() != SBML_LIST_OF || lorelist->getItemTypeCode() != SBML_COMP_REPLACEDELEMENT) {
if (doc) {
string error = "Cannot carry out replacement in ReplacedElement::performReplacement: no parent <listOfReplacedElements> could be found for the given replacement element.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_INVALID_OBJECT;
}
SBase* parent = lore->getParentSBMLObject();
if (parent==NULL) {
if (doc) {
string error = "Cannot carry out replacement in ReplacedElement::performReplacement: no parent could be found for the parent <listOfReplacedElements> object.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_INVALID_OBJECT;
}
SBase* ref = getReferencedElement();
if (ref==NULL) {
//getReferencedElement sets its own error messages.
return LIBSBML_INVALID_OBJECT;
}
if (removed && removed->find(ref)!=removed->end()) {
//Already deleted: can't get the deleted element's ID to
if (doc) {
string error = "Cannot carry out replacement in ReplacedElement::performReplacement: a <" + parent->getElementName() + ">";
if (parent->isSetId()) {
error += " with the ID '" + parent->getId() + "'";
}
error += " has a child <replacedElement> that points to something that has already been deleted, probably because its parent was deleted.";
doc->getErrorLog()->logPackageError("comp", CompDeletedReplacement, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_INVALID_OBJECT;
}
//Update the IDs.
int ret = updateIDs(ref, parent);
if (ret != LIBSBML_OPERATION_SUCCESS) {
return ret;
}
//Perform any conversions on references in the submodel.
ASTNode* blank = NULL;
ret = performConversions(parent, &blank);
if (ret != LIBSBML_OPERATION_SUCCESS)
{
if (blank != NULL)
{
delete blank;
}
return ret;
}
CompSBasePlugin* refplug = static_cast<CompSBasePlugin*>(ref->getPlugin(getPrefix()));
if (refplug != NULL) {
//Now recurse down the 'replace*' tree, renaming IDs and deleting things as we go.
for (unsigned int re=0; re<refplug->getNumReplacedElements(); re++) {
refplug->getReplacedElement(re)->replaceWithAndMaybeDelete(parent, true, blank);
if (toremove) {
toremove->insert(refplug->getReplacedElement(re)->getReferencedElement());
}
}
if (refplug->isSetReplacedBy()) {
//Even if the subelement used to be replaced by something further down, it is now being replaced by the parent. It just can't catch a break, it seems.
refplug->getReplacedBy()->replaceWithAndMaybeDelete(parent, true, blank);
if (toremove) {
toremove->insert(refplug->getReplacedBy()->getReferencedElement());
}
}
}
if (toremove) {
toremove->insert(ref);
}
if (blank != NULL)
{
delete blank;
}
return LIBSBML_OPERATION_SUCCESS;
}