/** @cond doxygenLibsbmlInternal */
void CompModelPlugin::renameIDs(List* allElements, const string& prefix)
{
if (prefix=="") return; //Nothing to prepend.
vector<pair<string, string> > renamedSIds;
vector<pair<string, string> > renamedUnitSIds;
vector<pair<string, string> > renamedMetaIds;
//PrefixTransformer trans(prefix);
for (unsigned long el=0; el < allElements->getSize(); ++el)
{
SBase* element = static_cast<SBase*>(allElements->get(el));
string id = element->getId();
string metaid = element->getMetaId();
//element->transformIdentifiers(&trans);
element->prependStringToAllIdentifiers(prefix);
if (element->getTypeCode() == SBML_LOCAL_PARAMETER) {
element->setId(id); //Change it back. This would perhaps be better served by overriding 'prependStringToAllIdentifiers' but hey.
}
string newid = element->getId();
string newmetaid = element->getMetaId();
if (id != newid) {
int type = element->getTypeCode();
if (type==SBML_UNIT_DEFINITION) {
renamedUnitSIds.push_back(make_pair(id, newid));
}
else if (type==SBML_COMP_PORT) {
//Do nothing--these can only be referenced from outside the Model, so they need to be handled specially.
// (In the default case, we throw them away).
}
else {
//This is a little dangerous, but hey! What's a little danger between friends!
//(What we are assuming is that any attribute you can get with 'getId' is of the type 'SId')
renamedSIds.push_back(make_pair(id, newid));
}
}
if (metaid != newmetaid) {
renamedMetaIds.push_back(make_pair(metaid, newmetaid));
}
}
for (unsigned long el=0; el<allElements->getSize(); el++) {
SBase* element = static_cast<SBase*>(allElements->get(el));
for (size_t id=0; id<renamedSIds.size(); id++)
{
element->renameSIdRefs(renamedSIds[id].first, renamedSIds[id].second);
}
for (size_t uid=0; uid<renamedUnitSIds.size(); uid++)
{
element->renameUnitSIdRefs(renamedUnitSIds[uid].first, renamedUnitSIds[uid].second);
}
for (size_t mid=0; mid<renamedMetaIds.size(); mid++)
{
element->renameMetaIdRefs(renamedMetaIds[mid].first, renamedMetaIds[mid].second);
}
}
}
int ReplacedBy::performReplacementAndCollect(set<SBase*>* removed, set<SBase*>* toremove)
{
SBMLDocument* doc = getSBMLDocument();
//Find the various objects and plugin objects we need for this to work.
SBase* parent = getParentSBMLObject();
if (parent==NULL) {
if (doc) {
string error = "Unable to perform replacement in ReplacedBy::performReplacement: no parent object for this <replacedBy> could be found.";
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;
}
//Update the IDs. (Will set its own error messages.)
int ret = updateIDs(ref, parent);
//ReplacedBy elements do get the name of the top-level element, assuming it has one:
if (parent->isSetId()) {
ref->setId(parent->getId());
}
if (parent->isSetMetaId()) {
ref->setMetaId(parent->getMetaId());
}
if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
//And finally, get ready to delete the parent object.
if (toremove) {
toremove->insert(parent);
}
return LIBSBML_OPERATION_SUCCESS;
}
int
SBMLIdConverter::convert()
{
if (mDocument == NULL) return LIBSBML_INVALID_OBJECT;
Model* mModel = mDocument->getModel();
if (mModel == NULL) return LIBSBML_INVALID_OBJECT;
// nothing to do
if (!mProps->hasOption("currentIds") || !mProps->hasOption("newIds"))
return LIBSBML_OPERATION_SUCCESS;
bool success = true;
IdList currentIds(mProps->getOption("currentIds")->getValue());
IdList newIds(mProps->getOption("newIds")->getValue());
// if the size does not match something is wrong.
if (newIds.size() != currentIds.size())
return LIBSBML_UNEXPECTED_ATTRIBUTE;
List* allElements = mDocument->getAllElements();
std::map<std::string, std::string> renamed;
// rename ids
for (unsigned int i = 0; i < allElements->getSize(); ++i)
{
SBase* current = static_cast<SBase*>(allElements->get(i));
if (current == NULL || !current->isSetId()
|| current->getTypeCode() == SBML_LOCAL_PARAMETER)
continue;
for (unsigned int j = 0; j < currentIds.size(); ++j)
{
if (current->getId() != currentIds.at((int)j))
continue;
// return error code in case new id is invalid
if (!SyntaxChecker::isValidSBMLSId(newIds.at((int)j)))
{
delete allElements;
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
}
current->setId(newIds.at((int)j));
renamed[currentIds.at((int)j)] = newIds.at((int)j);
break;
}
}
// update all references that we changed
std::map<std::string, std::string>::const_iterator it;
for (unsigned int i = 0; i < allElements->getSize(); ++i)
{
SBase* current = static_cast<SBase*>(allElements->get(i));
for (it = renamed.begin(); it != renamed.end(); ++it)
{
current->renameSIdRefs(it->first, it->second);
}
}
delete allElements;
if (success) return LIBSBML_OPERATION_SUCCESS;
return LIBSBML_OPERATION_FAILED;
}
LIBSBML_CPP_NAMESPACE_USE
BEGIN_C_DECLS
int
main (int argc, char* argv[])
{
if (argc != 5)
{
cout << endl << "Usage: renameSId filename oldSId newSId output" << endl << endl;
return 1;
}
const char* filename = argv[1];
const char* oldSId = argv[2];
const char* newSId = argv[3];
const char* output = argv[4];
if (strcmp(oldSId, newSId) == 0)
{
cout << "The Ids are identical, renaming stopped." << endl;
return 1;
}
if (!SyntaxChecker::isValidInternalSId(newSId))
{
cout << "The new SId '" << newSId
<< "' does not represent a valid SId."
<< endl;
return 1;
}
SBMLDocument* document;
SBMLReader reader;
#ifdef __BORLANDC__
unsigned long start, stop;
#else
unsigned long long start, stop;
#endif
start = getCurrentMillis();
document = reader.readSBML(filename);
stop = getCurrentMillis();
unsigned int errors = document->getNumErrors(LIBSBML_SEV_ERROR);
cout << endl;
cout << " filename: " << filename << endl;
cout << " file size: " << getFileSize(filename) << endl;
cout << " read time (ms): " << stop - start << endl;
cout << " error(s): " << errors << endl;
cout << endl;
if (errors > 0)
{
document->printErrors(cerr);
delete document;
return errors;
}
// find elements for old id
SBase* element = document->getElementBySId(oldSId);
if (element == NULL)
{
cout << "Found no element with SId '"
<< oldSId << "'." << endl;
return 1;
}
// found element --> renaming
element->setId(newSId);
// update all references to this element
List *allElements = document->getAllElements();
for (unsigned int i = 0; i < allElements->getSize(); ++i)
static_cast<SBase*>(allElements->get(i))->renameSIdRefs(oldSId, newSId);
// write to file
writeSBMLToFile(document, output);
delete document;
return errors;
}