int CompModelPlugin::saveAllReferencedElements(set<SBase*> uniqueRefs, set<SBase*> replacedBys)
{
SBMLDocument* doc = getSBMLDocument();
Model* model = static_cast<Model*>(getParentSBMLObject());
if (model==NULL) {
if (doc) {
string error = "Unable to discover any referenced elements in CompModelPlugin::saveAllReferencedElements: no Model parent of the 'comp' model plugin.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error);
}
return LIBSBML_OPERATION_FAILED;
}
int ret = LIBSBML_OPERATION_SUCCESS;
//Get a list of everything, pull out anything that's a deletion, replacement, or port, and save what they're pointing to.
//At the same time, make sure that no two things point to the same thing.
set<SBase*> RE_deletions = set<SBase*>(); //Deletions only point to things in the same model.
List* allElements = model->getAllElements();
string modname = "the main model in the document";
if (model->isSetId()) {
modname = "the model '" + model->getId() + "'";
}
set<SBase*> todelete;
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_DELETION ||
type==SBML_COMP_REPLACEDBY ||
type==SBML_COMP_REPLACEDELEMENT ||
type==SBML_COMP_PORT) {
//Don't worry about SBML_COMP_SBASEREF because they're all children of one of the above types.
SBaseRef* reference = static_cast<SBaseRef*>(element);
ReplacedElement* re = static_cast<ReplacedElement*>(element);
ret = reference->saveReferencedElement();
if (ret != LIBSBML_OPERATION_SUCCESS)
{
if (type != SBML_COMP_REPLACEDBY && doc)
{
SBMLErrorLog* errlog = doc->getErrorLog();
SBMLError* lasterr = const_cast<SBMLError*>
(doc->getErrorLog()->getError(doc->getNumErrors()-1));
if ( (errlog->contains(UnrequiredPackagePresent) ||
errlog->contains(RequiredPackagePresent)))
{
if ( lasterr->getErrorId() == CompIdRefMustReferenceObject)
{
//Change the error into a warning
string fullmsg = lasterr->getMessage()
+ " However, this may be because of the unrecognized "
+ "package present in this document: ignoring this "
+ "element and flattening anyway.";
errlog->remove(lasterr->getErrorId());
errlog->logPackageError("comp",
CompIdRefMayReferenceUnknownPackage, getPackageVersion(),
getLevel(), getVersion(), fullmsg, element->getLine(),
element->getColumn(), LIBSBML_SEV_WARNING);
}
else if ( lasterr->getErrorId() == CompMetaIdRefMustReferenceObject)
{
//Change the error into a warning
string fullmsg = lasterr->getMessage()
+ " However, this may be because of the unrecognized "
+ "package present in this document: ignoring this "
+ "element and flattening anyway.";
errlog->remove(lasterr->getErrorId());
errlog->logPackageError("comp",
CompMetaIdRefMayReferenceUnknownPkg, getPackageVersion(),
getLevel(), getVersion(), fullmsg, element->getLine(),
element->getColumn(), LIBSBML_SEV_WARNING);
}
}
//Whether or not we could figure out the error, we can always still continue flattening.
todelete.insert(element);
continue;
}
else {
delete allElements;
return ret;
}
}
SBase* direct = reference->getDirectReference();
bool adddirect = true;
if (type == SBML_COMP_REPLACEDBY) {
SBase* rbParent = reference->getParentSBMLObject();
if (uniqueRefs.insert(rbParent).second == false) {
if (doc) {
string error = "Error discovered in CompModelPlugin::saveAllReferencedElements when checking " + modname + ": a <" + rbParent->getElementName() + "> ";
if (direct->isSetId()) {
error += "with the id '" + rbParent->getId() + "'";
if (rbParent->isSetMetaId()) {
error += ", and the metaid '" + rbParent->getMetaId() + "'";
}
}
else if (rbParent->isSetMetaId()) {
error += "with the metaId '" + rbParent->getMetaId() + "'";
}
error += " has a <replacedBy> child and is also pointed to by a <port>, <deletion>, <replacedElement>, or one or more <replacedBy> objects.";
doc->getErrorLog()->logPackageError("comp", CompNoMultipleReferences, getPackageVersion(), getLevel(), getVersion(), error);
}
delete allElements;
return LIBSBML_OPERATION_FAILED;
}
adddirect = replacedBys.insert(direct).second;
}
if (type==SBML_COMP_REPLACEDELEMENT && re->isSetDeletion()) {
adddirect = RE_deletions.insert(direct).second;
}
if (adddirect) {
if (uniqueRefs.insert(direct).second == false) {
if (doc) {
string error = "Error discovered in CompModelPlugin::saveAllReferencedElements when checking " + modname + ": ";
if (replacedBys.find(direct) != replacedBys.end()) {
error += "one or more <replacedBy> elements, plus a <deletion>, <replacedElement>, or <port> element";
}
else if (RE_deletions.find(direct) != RE_deletions.end()) {
error += "one or more <replacedElement> elements using a 'deletion' attribute, plus a <deletion>, <replacedElement>, or <port> element";
}
else {
error += "multiple <deletion>, <replacedElement>, and/or <port> elements";
}
error += " point directly to the <" + direct->getElementName() + "> ";
if (direct->isSetId()) {
error += "with the id '" + direct->getId() + "'";
if (direct->isSetMetaId()) {
error += ", and the metaid '" + direct->getMetaId() + "'";
}
error += ".";
}
else if (direct->isSetMetaId()) {
error += "with the metaId '" + direct->getMetaId() + "'.";
}
doc->getErrorLog()->logPackageError("comp", CompNoMultipleReferences, getPackageVersion(), getLevel(), getVersion(), error);
}
delete allElements;
return LIBSBML_OPERATION_FAILED;
}
}
}
}
for(set<SBase*>::iterator el=todelete.begin(); el != todelete.end(); el++) {
(*el)->removeFromParentAndDelete();
}
delete allElements;
//Now call saveAllReferencedElements for all instantiated submodels.
for (unsigned long sm=0; sm<getNumSubmodels(); ++sm) {
Model* sub = getSubmodel((unsigned int)sm)->getInstantiation();
if (sub==NULL) {
return LIBSBML_OPERATION_FAILED;
}
CompModelPlugin* subplug = static_cast<CompModelPlugin*>(sub->getPlugin(getPrefix()));
if (subplug==NULL) {
return LIBSBML_OPERATION_FAILED;
}
ret = subplug->saveAllReferencedElements(uniqueRefs, replacedBys);
if (ret != LIBSBML_OPERATION_SUCCESS) {
return ret;
}
}
return LIBSBML_OPERATION_SUCCESS;
}
unsigned int operator() (const SBMLError& msg) {
return msg.getErrorId();
}
bool operator() (const SBMLError& msg) {
return msg.getErrorId() == id;
}
LIBSBML_CPP_NAMESPACE_USE
/** @endcond */
CK_CPPSTART
START_TEST (test_SBMLError_create)
{
SBMLError* error = new SBMLError;
fail_unless( error != NULL );
delete error;
error = new SBMLError(EmptyListInReaction);
fail_unless( error->getErrorId() == EmptyListInReaction );
fail_unless( error->getSeverity() == LIBSBML_SEV_ERROR );
fail_unless( error->getSeverityAsString() == "Error" );
fail_unless( error->getCategory() == LIBSBML_CAT_SBML );
fail_unless( error->getCategoryAsString() == "General SBML conformance");
fail_unless( error->isValid() == true);
delete error;
error = new SBMLError(OverdeterminedSystem, 2, 1);
fail_unless( error->getErrorId() == OverdeterminedSystem );
fail_unless( error->getSeverity() == LIBSBML_SEV_WARNING );
fail_unless( error->getSeverityAsString() == "Warning" );
fail_unless( error->getCategory() == LIBSBML_CAT_OVERDETERMINED_MODEL );
fail_unless( error->getCategoryAsString() == "Overdetermined model");
fail_unless( error->isValid() == true);
delete error;
error = new SBMLError(OffsetNoLongerValid, 2, 2);
fail_unless( error->getErrorId() == OffsetNoLongerValid );
fail_unless( error->getSeverity() == LIBSBML_SEV_ERROR );
fail_unless( error->getSeverityAsString() == "Error" );
fail_unless( error->getCategory() == LIBSBML_CAT_GENERAL_CONSISTENCY );
fail_unless( error->getCategoryAsString() == "SBML component consistency");
fail_unless( error->isValid() == true);
delete error;
error = new SBMLError(NoSBOTermsInL1, 2, 2);
fail_unless( error->getErrorId() == NoSBOTermsInL1 );
fail_unless( error->getSeverity() == LIBSBML_SEV_WARNING );
fail_unless( error->getSeverityAsString() == "Warning" );
fail_unless( error->getCategory() == LIBSBML_CAT_SBML_L1_COMPAT );
fail_unless( error->getCategoryAsString() == "Translation to SBML L1V2");
fail_unless( error->isValid() == true);
delete error;
error = new SBMLError(DisallowedMathMLEncodingUse, 2, 2);
fail_unless( error->getErrorId() == DisallowedMathMLEncodingUse );
fail_unless( error->getSeverity() == LIBSBML_SEV_ERROR );
fail_unless( error->getSeverityAsString() == "Error" );
fail_unless( error->getCategory() == LIBSBML_CAT_MATHML_CONSISTENCY );
fail_unless( error->getShortMessage() == "Use of the MathML 'encoding' attribute is not allowed on this element");
fail_unless( error->isValid() == true);
delete error;
error = new SBMLError(DisallowedMathMLEncodingUse, 1, 2);
fail_unless( error->getErrorId() == DisallowedMathMLEncodingUse );
fail_unless( error->getSeverity() == LIBSBML_SEV_NOT_APPLICABLE );
fail_unless( error->getCategory() == LIBSBML_CAT_MATHML_CONSISTENCY );
fail_unless( error->isValid() == true);
delete error;
error = new SBMLError(UnknownError, 2, 4);
fail_unless( error->getErrorId() == UnknownError );
fail_unless( error->getSeverity() == LIBSBML_SEV_FATAL );
fail_unless( error->getSeverityAsString() == "Fatal" );
fail_unless( error->getCategory() == LIBSBML_CAT_INTERNAL );
fail_unless( error->getShortMessage() == "Encountered unknown internal libSBML error");
fail_unless( error->isValid() == true);
delete error;
error = new SBMLError(70912, 2, 4);
fail_unless( error->getErrorId() == 70912 );
fail_unless( error->getSeverity() == LIBSBML_SEV_WARNING );
fail_unless( error->getSeverityAsString() == "Warning" );
fail_unless( error->getCategory() == LIBSBML_CAT_INTERNAL );
fail_unless( error->getShortMessage() == "Encountered unknown internal libSBML error");
fail_unless( error->isValid() == false);
delete error;
}