END_TEST
START_TEST (test_comp_sbase)
{
SBMLNamespaces sbmlns(3,1,"comp",1);
Parameter param(&sbmlns);
CompSBasePlugin* pplugin = static_cast<CompSBasePlugin*>(param.getPlugin("comp"));
fail_unless(pplugin->getNumReplacedElements()==0);
ReplacedElement* re = pplugin->createReplacedElement();
re->setMetaId("re1");
fail_unless(pplugin->getNumReplacedElements()==1);
fail_unless(pplugin->addReplacedElement(NULL)==LIBSBML_INVALID_OBJECT);
ReplacedElement re2(3, 1);
re2.setMetaId("re2");
fail_unless(pplugin->addReplacedElement(&re2)==LIBSBML_INVALID_OBJECT);
re2.setDeletion("ID1");
fail_unless(pplugin->addReplacedElement(&re2)==LIBSBML_INVALID_OBJECT);
re2.setSubmodelRef("mod1");
fail_unless(pplugin->addReplacedElement(&re2)==LIBSBML_OPERATION_SUCCESS);
ReplacedElement* reref = pplugin->getReplacedElement(1);
fail_unless(reref != NULL);
fail_unless(reref->getMetaId()=="re2");
reref = pplugin->getReplacedElement(0);
fail_unless(reref != NULL);
fail_unless(reref->getMetaId()=="re1");
re->setDeletion("ID1");
fail_unless(reref->getDeletion()=="ID1");
fail_unless(pplugin->removeReplacedElement(3)==NULL);
fail_unless(pplugin->removeReplacedElement(0)==re);
fail_unless(pplugin->getReplacedElement(1)==NULL);
fail_unless(pplugin->isSetReplacedBy()==false);
ReplacedBy* rb = pplugin->createReplacedBy();
fail_unless(rb != NULL);
fail_unless(pplugin->isSetReplacedBy()==true);
fail_unless(pplugin->setReplacedBy(NULL)==LIBSBML_OPERATION_SUCCESS);
fail_unless(pplugin->isSetReplacedBy()==false);
ReplacedBy rb2(3,1);
fail_unless(pplugin->setReplacedBy(&rb2)==LIBSBML_INVALID_OBJECT);
rb2.setIdRef("ID1");
fail_unless(pplugin->setReplacedBy(&rb2)==LIBSBML_INVALID_OBJECT);
rb2.setSubmodelRef("mod1");
fail_unless(pplugin->setReplacedBy(&rb2)==LIBSBML_OPERATION_SUCCESS);
fail_unless(pplugin->unsetReplacedBy()==LIBSBML_OPERATION_SUCCESS);
}
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;
}