int CompModelPlugin::collectDeletionsAndDeleteSome(set<SBase*>* removed, set<SBase*>* toremove)
{
int ret = LIBSBML_OPERATION_SUCCESS;
SBMLDocument* doc = getSBMLDocument();
Model* model = static_cast<Model*>(getParentSBMLObject());
if (model==NULL) {
if (doc) {
string error = "Unable to attempt to perform deletions in CompModelPlugin::collectDeletionsAndDeleteSome: no parent model could be found for the given 'comp' model plugin element.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error);
}
return LIBSBML_OPERATION_FAILED;
}
//Since deletions only exist in submodels, loop through the submodels.
for (unsigned int sub=0; sub<getNumSubmodels(); sub++) {
Submodel* submodel = getSubmodel(sub);
//First perform any deletions
for (unsigned int d=0; d<submodel->getNumDeletions(); d++) {
Deletion* deletion = submodel->getDeletion(d);
SBase* todel = deletion->getReferencedElement();
if (todel && (todel->getTypeCode() == SBML_COMP_DELETION ||
todel->getTypeCode() == SBML_COMP_REPLACEDBY ||
todel->getTypeCode() == SBML_COMP_REPLACEDELEMENT ||
todel->getTypeCode() == SBML_LOCAL_PARAMETER) )
{
//Go ahead and delete it!
set<SBase*> newToRemove;
newToRemove.insert(todel);
removeCollectedElements(removed, &newToRemove);
}
else {
//Otherwise, just collect it.
ret = deletion->collectDeletions(removed, toremove);
if (ret!=LIBSBML_OPERATION_SUCCESS) {
return ret;
}
}
}
//Next collect any deletions in that instantiated submodel (any that weren't just deleted)
Model* mod = submodel->getInstantiation();
if (mod==NULL) {
//getInstantiation sets its own error messages.
return LIBSBML_OPERATION_FAILED;
}
CompModelPlugin* modplug = static_cast<CompModelPlugin*>(mod->getPlugin(getPrefix()));
if (modplug==NULL) {
if (doc) {
//Shouldn't happen: 'getInstantiation' turns on the comp plugin.
string error = "Unable to rename elements in CompModelPlugin::collectDeletionsAndDeleteSome: no valid 'comp' plugin for the model instantiated from submodel " + submodel->getId();
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error);
}
return LIBSBML_OPERATION_FAILED;
}
modplug->collectDeletionsAndDeleteSome(removed, toremove);
}
return ret;
}
/*
* Loop through all Submodels in this Model, instantiate all of them,
* perform all deletions, and synchronize all replacements.
* The resulting models are stored in the Submodel objects,
* and available from 'Submodel::getInstantiation()'
*/
int
CompModelPlugin::instantiateSubmodels()
{
Model* model = static_cast<Model*>(getParentSBMLObject());
if (model==NULL)
return LIBSBML_INVALID_OBJECT;
int ret;
// First we instantiate all the submodels.
// This acts recursively downward through the stack.
for (unsigned int sub=0; sub<mListOfSubmodels.size(); sub++)
{
Submodel* submodel = mListOfSubmodels.get(sub);
// Instead of 'instantiate', since we might have already
// been instantiated ourselves from above.
Model* submodinst = submodel->getInstantiation();
if (submodinst == NULL ) {
//'getInstantiation' already sets any errors that might have occurred.
return LIBSBML_OPERATION_FAILED;
}
//// if we have a transformer specified, then we need to propagate it, so it can
//// be used
// this needs to happen in Submodel:instantiate
//if (isSetTransformer())
//{
// CompModelPlugin* other = dynamic_cast<CompModelPlugin*>(submodinst->getPlugin("comp"));
// if (other != NULL)
// other->setTransformer(getTransformer());
//}
}
// Next, recursively find all the targets of SBaseRef elements
// and save them, since we're about to rename everything and
// we won't be able to find things by name any more.
ret = saveAllReferencedElements();
if (ret != LIBSBML_OPERATION_SUCCESS) {
//saveAllReferencedElements sets any errors.
return ret;
}
mRemoved.clear();
set<SBase*> toremove;
// Collect deletions (top-down):
// need to do this before renaming in case we delete a local parameter.
ret = collectDeletionsAndDeleteSome(&mRemoved, &toremove);
if (ret != LIBSBML_OPERATION_SUCCESS) {
return ret;
}
//Next, we rename *all* the elements so everything is unique.
ret = renameAllIDsAndPrepend("");
if (ret != LIBSBML_OPERATION_SUCCESS) {
return ret;
}
//Perform replacements and conversions (top-down) and collect them.
ret = collectRenameAndConvertReplacements(&mRemoved, &toremove);
if (ret != LIBSBML_OPERATION_SUCCESS) {
return ret;
}
//Finally, actually remove the collected elements from the model--they are
// all now redundant. Have to wait until now to do this, because of the
// possibility of nested constructs: replacing the child of a replaced
// element, for example, or even replacing the child of a deleted
// element.
removeCollectedElements(&mRemoved, &toremove);
mRemoved.clear();
return LIBSBML_OPERATION_SUCCESS;
}
int CompModelPlugin::collectRenameAndConvertReplacements(set<SBase*>* removed, set<SBase*>* toremove)
{
int ret = LIBSBML_OPERATION_SUCCESS;
SBMLDocument* doc = getSBMLDocument();
Model* model = static_cast<Model*>(getParentSBMLObject());
if (model==NULL) {
if (doc) {
string error = "Unable to perform replacements in CompModelPlugin::collectRenameAndConvertReplacements: no parent model could be found for the given 'comp' model plugin element.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error);
}
return LIBSBML_OPERATION_FAILED;
}
List* allElements = model->getAllElements();
vector<ReplacedElement*> res;
vector<ReplacedBy*> rbs;
//Collect replaced elements and replaced by's.
for (unsigned int e=0; e<allElements->getSize(); e++) {
SBase* element = static_cast<SBase*>(allElements->get(e));
int type = element->getTypeCode();
if (type==SBML_COMP_REPLACEDELEMENT) {
ReplacedElement* reference = static_cast<ReplacedElement*>(element);
res.push_back(reference);
}
if (type==SBML_COMP_REPLACEDBY) {
ReplacedBy* reference = static_cast<ReplacedBy*>(element);
rbs.push_back(reference);
}
}
delete allElements;
//ReplacedElement replacements
for (size_t re=0; re<res.size(); re++) {
ret = res[re]->performReplacementAndCollect(removed, toremove);
if (ret != LIBSBML_OPERATION_SUCCESS) {
return ret;
}
}
//Now do the same thing for anything left over in the submodels
for (unsigned int sub=0; sub<getNumSubmodels(); sub++) {
Submodel* submodel = getSubmodel(sub);
Model* mod = submodel->getInstantiation();
if (mod==NULL) return LIBSBML_OPERATION_FAILED;
CompModelPlugin* modplug = static_cast<CompModelPlugin*>(mod->getPlugin(getPrefix()));
if (modplug==NULL) return LIBSBML_OPERATION_FAILED;
//'left behind' converions (not LaHaye-style)
ret = submodel->convertTimeAndExtent();
if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
ret = modplug->collectRenameAndConvertReplacements(removed, toremove);
if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
}
//Perform ReplacedBy replacements *after* the submodels are done, so that the topmost-level names take precedence.
for (size_t rb=0; rb<rbs.size(); rb++) {
ret = rbs[rb]->performReplacementAndCollect(removed, toremove);
if (ret != LIBSBML_OPERATION_SUCCESS) {
return ret;
}
}
return ret;
}
int
Replacing::saveReferencedElement()
{
SBMLDocument* doc = getSBMLDocument();
if (!isSetSubmodelRef()) {
if (doc) {
string error = "Unable to find referenced element in Replacing::saveReferencedElement: the given <" + getElementName() + "> element";
if (isSetId()) {
error += " '" + getId() + "'";
}
error += " has no 'submodelRef' attribute.";
doc->getErrorLog()->logPackageError("comp", CompReplacedElementAllowedAttributes, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_INVALID_OBJECT;
}
Model* model = getParentModel(this);
if (model==NULL) {
if (doc) {
string error = "Unable to find referenced element in Replacing::saveReferencedElement: no parent model could be found for the given <" + getElementName() + "> element";
if (isSetId()) {
error += " '" + getId() + "'.";
}
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_OPERATION_FAILED;
}
CompModelPlugin* cmp = static_cast<CompModelPlugin*>(model->getPlugin(getPrefix()));
if (cmp==NULL) {
if (doc) {
string error = "Unable to find referenced element in Replacing::saveReferencedElement: no 'comp' plugin for the parent model could be found for the given <" + getElementName() + "> element";
if (isSetId()) {
error += " '" + getId() + "'.";
}
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_OPERATION_FAILED;
}
Submodel* submod = cmp->getSubmodel(getSubmodelRef());
if (submod==NULL) {
if (doc) {
string error = "Unable to find referenced element for the given <" + getElementName() + "> element";
if (isSetId()) {
error += " '" + getId() + "'";
}
error += " in Replacing::saveReferencedElement: the submodelRef '" + getSubmodelRef() + "' could not be found in the model.";
int errnumber = CompReplacedElementSubModelRef;
if (getTypeCode() == SBML_COMP_REPLACEDBY) {
errnumber = CompReplacedBySubModelRef;
}
doc->getErrorLog()->logPackageError("comp", errnumber, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
}
Model* inst = submod->getInstantiation();
if (inst==NULL) {
//getInstantiation sets it own error messages.
return LIBSBML_OPERATION_FAILED;
}
mReferencedElement = getReferencedElementFrom(inst);
if (mDirectReference==NULL) {
mDirectReference = mReferencedElement;
}
//getReferencedElement* set their own error messages:
if (mReferencedElement==NULL) {
return LIBSBML_OPERATION_FAILED;
}
if (mReferencedElement->getTypeCode()==SBML_COMP_PORT) {
mReferencedElement = static_cast<Port*>(mReferencedElement)->getReferencedElement();
}
if (mReferencedElement==NULL) {
return LIBSBML_OPERATION_FAILED;
}
return LIBSBML_OPERATION_SUCCESS;
}
SBase*
SBaseRef::getReferencedElementFrom(Model* model)
{
SBMLDocument* doc = getSBMLDocument();
if (!hasRequiredAttributes()) {
if (doc) {
string error = "In SBaseRef::getReferencedElementFrom, unable to find referenced element from <" + getElementName() + "> ";
if (isSetId()) {
error += "with ID '" + getId() + "' ";
}
error += "as it does not have the required attributes.";
int en = CompSBaseRefMustReferenceObject;
switch(getTypeCode()) {
case SBML_COMP_REPLACEDBY:
en = CompReplacedByAllowedAttributes;
break;
case SBML_COMP_REPLACEDELEMENT:
en = CompReplacedElementAllowedAttributes;
break;
case SBML_COMP_PORT:
en = CompPortAllowedAttributes;
break;
case SBML_COMP_DELETION:
en = CompDeletionAllowedAttributes;
}
doc->getErrorLog()->logPackageError("comp", en, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return NULL;
}
SBase* referent = NULL;
if (isSetPortRef()) {
CompModelPlugin* mplugin = static_cast<CompModelPlugin*>(model->getPlugin(getPrefix()));
Port* port = mplugin->getPort(getPortRef());
if (port==NULL) {
if (doc) {
string error = "In SBaseRef::getReferencedElementFrom, unable to find referenced element from SBase reference ";
if (isSetId()) {
error += "'" + getId() + "' ";
}
error += "as the port it references ('" + getPortRef() +"') could not be found.";
doc->getErrorLog()->logPackageError("comp", CompPortRefMustReferencePort, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return NULL;
}
mDirectReference = port;
referent = port->getReferencedElementFrom(model);
}
else if (isSetIdRef()) {
referent = model->getElementBySId(getIdRef());
if (referent == NULL && doc) {
string error = "In SBaseRef::getReferencedElementFrom, unable to find referenced element: no such SId in the model: '" + getIdRef() + "'.";
if (doc->getErrorLog()->contains(UnrequiredPackagePresent)
|| doc->getErrorLog()->contains(RequiredPackagePresent))
{
doc->getErrorLog()->logPackageError("comp",
CompIdRefMayReferenceUnknownPackage, getPackageVersion(),
getLevel(), getVersion(), error, getLine(), getColumn());
}
else
{
doc->getErrorLog()->logPackageError("comp",
CompIdRefMustReferenceObject, getPackageVersion(),
getLevel(), getVersion(), error, getLine(), getColumn());
}
}
}
else if (isSetUnitRef()) {
referent = model->getUnitDefinition(getUnitRef());
if (referent == NULL && doc) {
string error = "In SBaseRef::getReferencedElementFrom, unable to find referenced element: no such Unit in the model: '" + getUnitRef() + "'.";
doc->getErrorLog()->logPackageError("comp", CompUnitRefMustReferenceUnitDef, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
}
else if (isSetMetaIdRef()) {
referent = model->getElementByMetaId(getMetaIdRef());
if (referent == NULL && doc) {
string error = "In SBaseRef::getReferencedElementFrom, unable to find referenced element: no such metaid in the model: '" + getMetaIdRef() + "'.";
if (doc->getErrorLog()->contains(UnrequiredPackagePresent)
|| doc->getErrorLog()->contains(RequiredPackagePresent))
{
doc->getErrorLog()->logPackageError("comp",
CompIdRefMayReferenceUnknownPackage, getPackageVersion(),
getLevel(), getVersion(), error, getLine(), getColumn());
}
else
{
doc->getErrorLog()->logPackageError("comp",
CompMetaIdRefMustReferenceObject, getPackageVersion(),
getLevel(), getVersion(), error, getLine(), getColumn());
}
}
}
else {
//This is actually possible if the subclass overrides getNumReferents() (which some do). In that case, we just return NULL and let the overriding function find the referent instead.
return NULL;
}
if (referent == NULL) {
//No need to set an error message--one was already set above.
return NULL;
}
if (isSetSBaseRef()) {
//We're drilling into the submodels here, so our referent must be a submodel.
if (referent->getTypeCode() != SBML_COMP_SUBMODEL) {
if (doc) {
string error = "In SBaseRef::getReferencedElementFrom, unable to find referenced element: the element ";
if (referent->isSetId()) {
error += "'" + referent->getId() + "'";
}
else if (referent->isSetMetaId()) {
error += "with the metaid '" + referent->getMetaId() + "'";
}
error += " is not a submodel, and therefore has no subobjects for the child <sBaseRef> to refer to.";
doc->getErrorLog()->logPackageError("comp", CompParentOfSBRefChildMustBeSubmodel, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return NULL;
}
Submodel* subm = static_cast<Submodel*>(referent);
if (subm==NULL) {
//Note: should be impossible.
if (doc) {
string error = "In SBaseRef::getReferencedElementFrom, unable to find referenced element: the element ";
if (referent->isSetId()) {
error += "'" + referent->getId() + "' ";
}
else if (referent->isSetMetaId()) {
error += "with the metaid '" + referent->getMetaId() + "' ";
}
error += "claims to be a Submodel, but could not be programmatically turned into one.";
doc->getErrorLog()->logPackageError("comp", CompParentOfSBRefChildMustBeSubmodel, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return NULL;
}
Model* inst = subm->getInstantiation();
if (inst==NULL) {
//No need to set an additional error, as 'getInstantiation' will set one itself.
return NULL;
}
//Recursive, so will set its own error messages:
referent = getSBaseRef()->getReferencedElementFrom(inst);
mDirectReference = getSBaseRef()->getDirectReference();
}
return referent;
}
