static SBMLDocument *checkedReadSBMLFromString(const char* xml)
{
SBMLDocument *doc = readSBMLFromString(xml);
if (doc)
{
if (doc->getModel() == 0)
{
// fatal error
SBMLErrorLog *log = doc->getErrorLog();
string errors = log ? log->toString() : " NULL SBML Error Log";
delete doc;
throw_llvm_exception("Fatal SBML error, no model, errors in sbml document: " + errors);
}
else if (doc->getNumErrors() > 0)
{
SBMLErrorLog *log = doc->getErrorLog();
string errors = log ? log->toString() : " NULL SBML Error Log";
Log(rr::Logger::LOG_WARNING) << "Warning, errors found in sbml document: " + errors;
}
}
else
{
delete doc;
throw_llvm_exception("readSBMLFromString returned NULL, no further information available");
}
return doc;
}
SBMLDocument_t *
convertModel (SBMLDocument_t *d1)
{
char *model;
SBMLDocument_t *d2;
SBMLDocument_setLevel(d1, 2);
SBMLDocument_setVersion(d1, 1);
model = writeSBMLToString(d1);
d2 = readSBMLFromString(model);
free(model);
return d2;
}
std::string fixMissingStoich(const std::string sbml) {
SBMLDocument *doc = NULL;
try {
doc = readSBMLFromString (sbml.c_str());
Model *m = doc->getModel();
for (int j = 0; j<m->getNumReactions(); ++j) {
Reaction* r = m->getReaction(j);
if (!r)
throw std::runtime_error("No reaction");
// check stoich defined on reactants / products
for (int k = 0; k<r->getNumReactants(); ++k) {
SpeciesReference* s = r->getReactant(k);
if (!isStoichDefined(s))
if (s->setStoichiometry(1.) != LIBSBML_OPERATION_SUCCESS)
throw std::runtime_error("Unable to set stoichiometry");
}
for (int k = 0; k<r->getNumProducts(); ++k) {
SpeciesReference* s = r->getProduct(k);
if (!isStoichDefined(s))
if (s->setStoichiometry(1.) != LIBSBML_OPERATION_SUCCESS)
throw std::runtime_error("Unable to set stoichiometry");
}
// modifiers have no stoichiometry
}
} catch(...) {
delete doc;
throw;
}
SBMLWriter writer;
char* sbml_cstr = writer.writeSBMLToString(doc);
delete doc;
std::string result(sbml_cstr);
free(sbml_cstr);
return result;
}
std::string validateSBML(const std::string src, unsigned opt)
{
std::stringstream errors;
SBMLDocument *doc = NULL;
try {
string sbml = SBMLReader::read(src);
doc = readSBMLFromString (sbml.c_str());
doc->setConsistencyChecks(LIBSBML_CAT_GENERAL_CONSISTENCY,
opt & VALIDATE_GENERAL);
doc->setConsistencyChecks(LIBSBML_CAT_UNITS_CONSISTENCY,
opt & VALIDATE_UNITS);
doc->setConsistencyChecks(LIBSBML_CAT_IDENTIFIER_CONSISTENCY,
opt & VALIDATE_IDENTIFIER);
doc->setConsistencyChecks(LIBSBML_CAT_MATHML_CONSISTENCY,
opt & VALIDATE_MATHML);
doc->setConsistencyChecks(LIBSBML_CAT_OVERDETERMINED_MODEL,
opt & VALIDATE_OVERDETERMINED);
doc->setConsistencyChecks(LIBSBML_CAT_MODELING_PRACTICE,
opt & VALIDATE_MODELING_PRACTICE);
doc->checkConsistency();
SBMLErrorLog* errorLog = doc->getErrorLog();
if(errorLog) {
errorLog->printErrors(errors);
}
} catch(...) {
delete doc;
throw;
}
delete doc;
return errors.str();
}
// Return true if stoichiometry is defined for every reaction in the model
bool isStoichDefined(const std::string sbml) {
SBMLDocument *doc = NULL;
bool sbml_decl_okay = false;
// check for <?xml
size_t pos = sbml.find("<");
if (pos != std::string::npos) {
pos = sbml.find("?", pos+1);
if (pos != std::string::npos) {
pos = sbml.find("xml", pos+1);
if (pos != std::string::npos)
sbml_decl_okay = true;
}
}
// check for <sbml
pos = sbml.find("<");
if (pos != std::string::npos) {
pos = sbml.find("sbml", pos+1);
if (pos != std::string::npos)
sbml_decl_okay = true;
}
if (!sbml_decl_okay)
throw std::runtime_error("SBML document must begin with an XML declaration or an SBML declaration");
try {
doc = readSBMLFromString (sbml.c_str());
if (!doc)
throw std::runtime_error("Unable to read SBML");
if (doc->getLevel() < 3)
return true; // stoichiometry has a default value in level 1 & 2
const Model *m = doc->getModel();
if (!m)
throw std::runtime_error("SBML string invalid or missing model");
for (int j = 0; j<m->getNumReactions(); ++j) {
const Reaction* r = m->getReaction(j);
if (!r)
throw std::runtime_error("No reaction");
// check stoich defined on reactants / products
for (int k = 0; k<r->getNumReactants(); ++k) {
if (!isStoichDefined(r->getReactant(k)))
return false;
}
for (int k = 0; k<r->getNumProducts(); ++k) {
if (!isStoichDefined(r->getProduct(k)))
return false;
}
// modifiers have no stoichiometry
}
} catch(...) {
delete doc;
throw;
}
delete doc;
return true;
}
