/*
* Logs a message about the conditional part of a piecewise function
* that should have dimensionless units
*/
void
ArgumentsUnitsCheck::logInconsistentPiecewiseCondition (const ASTNode & node,
const SBase & sb)
{
char * formula = SBML_formulaToString(&node);
msg = "The formula '";
msg += formula;
msg += "' in the math element of the <";
msg += sb.getElementName();
msg += "> ";
switch(sb.getTypeCode()) {
case SBML_INITIAL_ASSIGNMENT:
case SBML_EVENT_ASSIGNMENT:
case SBML_ASSIGNMENT_RULE:
case SBML_RATE_RULE:
//LS DEBUG: could use other attribute values, or 'isSetActualId'.
break;
default:
if (sb.isSetId()) {
msg += "with id '";
msg += sb.getId() + "' ";
}
break;
}
msg += "uses a piecewise function";
msg += " where the conditional statement is not dimensionless.";
safe_free(formula);
logFailure(sb, msg);
}
/*
* @return the error message to use when logging constraint violations.
* This method is called by logFailure.
*
* Returns a message that the given @p id and its corresponding object are
* in conflict with an object previously defined.
*/
const string
CiElementMathCheck::getMessage (const ASTNode& node, const SBase& object)
{
ostringstream msg;
//msg << getPreamble();
char * formula = SBML_formulaToString(&node);
msg << "The formula '" << formula;
msg << "' in the " << getFieldname() << " element of the <" << object.getElementName();
msg << "> ";
switch(object.getTypeCode()) {
case SBML_INITIAL_ASSIGNMENT:
case SBML_EVENT_ASSIGNMENT:
case SBML_ASSIGNMENT_RULE:
case SBML_RATE_RULE:
//LS DEBUG: could use other attribute values, or 'isSetActualId'.
break;
default:
if (object.isSetId()) {
msg << "with id '" << object.getId() << "' ";
}
break;
}
if (object.getLevel() == 2 && object.getVersion() == 1)
msg << "uses '" << node.getName() << "' that is not the id of a species/compartment/parameter.";
else if (object.getLevel() < 3)
msg << "uses '" << node.getName() << "' that is not the id of a species/compartment/parameter/reaction.";
else
msg << "uses '" << node.getName() << "' that is not the id of a species/compartment/parameter/reaction/speciesReference.";
safe_free(formula);
return msg.str();
}
/*
* @return the error message to use when logging constraint violations.
* This method is called by logFailure.
*
* Returns a message that the given @p id and its corresponding object are
* in conflict with an object previously defined.
*/
const string
FunctionApplyMathCheck::getMessage (const ASTNode& node, const SBase& object)
{
ostringstream msg;
//msg << getPreamble();
char * formula = SBML_formulaToString(&node);
msg << "The formula '" << formula;
msg << "' in the " << getFieldname() << " element of the <" << object.getElementName();
msg << "> ";
switch(object.getTypeCode()) {
case SBML_INITIAL_ASSIGNMENT:
case SBML_EVENT_ASSIGNMENT:
case SBML_ASSIGNMENT_RULE:
case SBML_RATE_RULE:
//LS DEBUG: could use other attribute values, or 'isSetActualId'.
break;
default:
if (object.isSetId()) {
msg << "with id '" << object.getId() << "' ";
}
break;
}
msg << "uses '" << node.getName() << "' which is not a function definition id.";
safe_free(formula);
return msg.str();
}
/*
* Logs a message about a function that should return same units
* as the arguments
*/
void
ArgumentsUnitsCheck::logInconsistentSameUnits (const ASTNode & node,
const SBase & sb)
{
char * formula = SBML_formulaToString(&node);
msg = "The formula '" ;
msg += formula;
msg += "' in the math element of the <";
msg += sb.getElementName();
msg += "> ";
switch(sb.getTypeCode()) {
case SBML_INITIAL_ASSIGNMENT:
case SBML_EVENT_ASSIGNMENT:
case SBML_ASSIGNMENT_RULE:
case SBML_RATE_RULE:
//LS DEBUG: could use other attribute values, or 'isSetActualId'.
break;
default:
if (sb.isSetId()) {
msg += "with id '";
msg += sb.getId() + "' ";
}
break;
}
msg += "can only act on variables with the same units.";
safe_free(formula);
logFailure(sb, msg);
}
/*
* @return the error message to use when logging constraint violations.
* This method is called by logFailure.
*
* Returns a message that the given @p id and its corresponding object are
* in conflict with an object previously defined.
*/
const string
ArgumentsUnitsCheck::getMessage (const ASTNode& node, const SBase& object)
{
ostringstream msg;
//msg << getPreamble();
char * formula = SBML_formulaToString(&node);
msg << "The formula '" << formula;
msg << "' in the " << getFieldname() << " element of the <" << object.getElementName();
msg << "> ";
switch(object.getTypeCode()) {
case SBML_INITIAL_ASSIGNMENT:
case SBML_EVENT_ASSIGNMENT:
case SBML_ASSIGNMENT_RULE:
case SBML_RATE_RULE:
//LS DEBUG: could use other attribute values, or 'isSetActualId'.
break;
default:
if (object.isSetId()) {
msg << "with id '" << object.getId() << "' ";
}
break;
}
msg << "produces an exponent that is not an integer and thus may produce ";
msg << "invalid units.";
safe_free(formula);
return msg.str();
}
/*
* @return the error message to use when logging constraint violations.
* This method is called by logFailure.
*
* Returns a message that the given @p id and its corresponding object are
* in conflict with an object previously defined.
*/
const string
NumericArgsMathCheck::getMessage (const ASTNode& node, const SBase& object)
{
ostringstream msg;
//msg << getPreamble();
char * formula = SBML_formulaToString(&node);
msg << "The formula '" << formula;
msg << "' in the " << getFieldname() << " element of the <" << object.getElementName();
msg << "> ";
switch(object.getTypeCode()) {
case SBML_INITIAL_ASSIGNMENT:
case SBML_EVENT_ASSIGNMENT:
case SBML_ASSIGNMENT_RULE:
case SBML_RATE_RULE:
//LS DEBUG: could use other attribute values, or 'isSetActualId'.
break;
default:
if (object.isSetId()) {
msg << "with id '" << object.getId() << "' ";
}
break;
}
msg << "uses an argument to a operator that expects a numeric value.";
safe_free(formula);
return msg.str();
}
/*
* @return the error message to use when logging constraint violations.
* This method is called by logFailure.
*
* Returns a message that the given @p id and its corresponding object are
* in conflict with an object previously defined.
*/
const string
PieceBooleanMathCheck::getMessage (const ASTNode& node, const SBase& object)
{
ostringstream oss_msg;
//oss_msg << getPreamble();
char * formula = SBML_formulaToString(&node);
oss_msg << "The formula '" << formula;
oss_msg << "' in the " << getFieldname() << " element of the <" << object.getElementName();
oss_msg << "> ";
switch(object.getTypeCode()) {
case SBML_INITIAL_ASSIGNMENT:
case SBML_EVENT_ASSIGNMENT:
case SBML_ASSIGNMENT_RULE:
case SBML_RATE_RULE:
//LS DEBUG: could use other attribute values, or 'isSetActualId'.
break;
default:
if (object.isSetId()) {
oss_msg << "with id '" << object.getId() << "' ";
}
break;
}
oss_msg << "uses a piecewise function that does not return a Boolean.";
safe_free(formula);
return oss_msg.str();
}
/*
* @return the error message to use when logging constraint violations.
* This method is called by logFailure.
*
* Returns a message that the given @p id and its corresponding object are
* in conflict with an object previously defined.
*/
const string
GroupsUniqueModelWideIds::getMessage (const string& id, const SBase& object)
{
IdObjectMap::iterator iter = mIdMap.find(id);
if (iter == mIdMap.end())
{
return
"Internal (but non-fatal) Validator error in "
"GroupsUniqueModelWideIds::getMessage(). The SBML object with duplicate id was "
"not found when it came time to construct a descriptive error message.";
}
ostringstream msg;
const SBase& previous = *(iter->second);
//msg << getPreamble();
//
// Example message:
//
// The <compartment> id 'cell' conflicts with the previously defined
// <parameter> id 'cell' at line 10.
//
msg << " The <" << object.getElementName()
<< "> id '" << id << "' conflicts with the previously defined <"
<< previous.getElementName()
<< "> id '" << id << "'";
if (previous.getLine() != 0)
{
msg << " at line " << previous.getLine();
}
msg << '.';
return msg.str();
}
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;
}
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;
}