List*
Submodel::getAllInstantiatedElements()
{
Model* inst = getInstantiation();
if (inst==NULL) return NULL;
List* allElements = inst->getAllElements();
vector<List*> sublists;
CompModelPlugin* instp = static_cast<CompModelPlugin*>(inst->getPlugin(getPrefix()));
for (unsigned int sm=0; sm<instp->getNumSubmodels(); sm++) {
Submodel* subm=instp->getSubmodel(sm);
if (subm==NULL) return NULL;
List* sublist = subm->getAllInstantiatedElements();
sublists.push_back(sublist);
}
for (size_t l=0; l<sublists.size(); l++) {
allElements->transferFrom(sublists[l]);
delete sublists[l];
}
return allElements;
}
SBase*
ReplacedElement::getReferencedElementFrom(Model* model)
{
SBMLDocument* doc = getSBMLDocument();
SBase* referent = Replacing::getReferencedElementFrom(model);
if (referent != NULL) return referent;
if (!isSetDeletion()) {
//In this case, something else went wrong in getReferencedElementFrom, which will have set its own error message.
return NULL;
}
model = getParentModel(this);
if (model==NULL) {
if (doc) {
string error = "In ReplacedElement::getReferencedElementFrom, unable to find referenced deletion '" + getDeletion() + "' for <replacedElement>: no parent model could be found.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return NULL;
}
CompModelPlugin* mplugin = static_cast<CompModelPlugin*>(model->getPlugin(getPrefix()));
if (mplugin==NULL) {
if (doc) {
string error = "In ReplacedElement::getReferencedElementFrom, unable to find referenced deletion '" + getDeletion() + "' for <replacedElement>: no 'comp' plugin for the parent model could be found.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return NULL;
}
Submodel* submod = mplugin->getSubmodel(getSubmodelRef());
if (submod==NULL) {
if (doc) {
string error = "In ReplacedElement::getReferencedElementFrom, unable to find referenced deletion '" + getDeletion() + "' for <replacedElement>: no such submodel '" + getSubmodelRef() + "'.";
doc->getErrorLog()->logPackageError("comp", CompReplacedElementSubModelRef, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return NULL;
}
SBase* ret = submod->getDeletion(getDeletion());
if (ret==NULL && doc) {
string error = "In ReplacedElement::getReferencedElementFrom, unable to find referenced deletion '" + getDeletion() + "' for <replacedElement>: no deletion with that ID exists in the model.";
doc->getErrorLog()->logPackageError("comp", CompDeletionMustReferenceObject, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return ret;
}
Model* CompModelPlugin::flattenModel() const
{
//First make a copy of our parent (the model to be flattened):
const Model* parent = static_cast<const Model*>(getParentSBMLObject());
if (parent==NULL) {
return NULL;
}
//doc needs to be non-const so that the error messages can be updated. Otherwise, nothing changes.
SBMLDocument* doc = const_cast<SBMLDocument*>(getSBMLDocument());
if (doc==NULL) {
return NULL;
}
//Set the original document so that it can find the model definitions
//and external model definitions while we flatten.
Model* flat = parent->clone();
flat->setSBMLDocument(doc);
CompModelPlugin* flatplug =
static_cast<CompModelPlugin*>(flat->getPlugin(getPrefix()));
// Now instantiate its submodels and
// follow all renaming/deletion/replacement rules.
vector<const Model*> submods;
int success = flatplug->instantiateSubmodels();
if (success != LIBSBML_OPERATION_SUCCESS) {
//instantiateSubmodels sets its own error messages.
delete flat;
return NULL;
}
//Now start the aggregation process.
//This goes from the bottom up, calling 'appendFrom' iteratively
//(from the plugin).
for (unsigned int sm=0; sm<flatplug->getNumSubmodels(); sm++)
{
Model* submodel = flatplug->getSubmodel(sm)->getInstantiation();
if (submodel==NULL) {
//getInstantiation should be calling a cached value by now, but if not, it will set its own error messages.
delete flat;
return NULL;
}
CompModelPlugin* submodplug =
static_cast<CompModelPlugin*>(submodel->getPlugin(getPrefix()));
if (submodplug != NULL) {
//Strip the ports from the submodel, as we no longer need them.
while (submodplug->getNumPorts() > 0)
{
delete submodplug->removePort(0);
}
}
success = flat->appendFrom(submodel);
if (success != LIBSBML_OPERATION_SUCCESS) {
string error = "Unable to flatten model in CompModelPlugin::flattenModel: appending elements from the submodel '" + submodel->getId() + "' to the elements of the parent model failed.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error);
delete flat;
return NULL;
}
}
// Now we clear the saved referenced elements in the local Port objects,
// but point them to the new object if necessary.
flatplug->resetPorts();
// Next, strip the package info from 'flat'.
// We're going to remove everything but the Ports:
flatplug->mListOfSubmodels.clear();
flatplug->clearReplacedElements();
flatplug->unsetReplacedBy();
List* allelements = flat->getAllElements();
vector<SBase*> nonReplacedElements;
for (unsigned int el=0; el<allelements->getSize(); el++)
{
SBase* element = static_cast<SBase*>(allelements->get(el));
int type = element->getTypeCode();
if (!(type==SBML_COMP_REPLACEDBY ||
type==SBML_COMP_REPLACEDELEMENT ||
type==SBML_COMP_SBASEREF))
{
nonReplacedElements.push_back(element);
}
}
// delete the list
delete allelements;
for (unsigned int el=0; el<nonReplacedElements.size(); el++)
{
SBase* element = nonReplacedElements[el];
CompSBasePlugin* elplug =
static_cast<CompSBasePlugin*>(element->getPlugin(getPrefix()));
if (elplug != NULL)
{
elplug->clearReplacedElements();
elplug->unsetReplacedBy();
}
}
//Finally, unset the document again.
flat->setSBMLDocument(NULL);
return flat;
}
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;
}
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;
}