ModelGeneratorContext::ModelGeneratorContext(std::string const &sbml,
unsigned options) :
ownedDoc(0),
doc(0),
symbols(0),
modelSymbols(0),
errString(new string()),
context(0),
executionEngine(0),
module(0),
builder(0),
functionPassManager(0),
options(options),
moietyConverter(0)
{
try
{
ownedDoc = checkedReadSBMLFromString(sbml.c_str());
if (options & rr::ModelGenerator::CONSERVED_MOIETIES)
{
if ((rr::Config::getInt(rr::Config::ROADRUNNER_DISABLE_WARNINGS) &
rr::Config::ROADRUNNER_DISABLE_WARNINGS_CONSERVED_MOIETY) == 0)
{
Log(Logger::LOG_NOTICE) << "performing conserved moiety conversion";
}
// check if already conserved doc
if (rr::conservation::ConservationExtension::isConservedMoietyDocument(ownedDoc))
{
doc = ownedDoc;
}
else
{
moietyConverter = new rr::conservation::ConservedMoietyConverter();
if (moietyConverter->setDocument(ownedDoc) != LIBSBML_OPERATION_SUCCESS)
{
throw_llvm_exception("error setting conserved moiety converter document");
}
if (moietyConverter->convert() != LIBSBML_OPERATION_SUCCESS)
{
throw_llvm_exception("error converting document to conserved moieties");
}
doc = moietyConverter->getDocument();
SBMLWriter sw;
char* convertedStr = sw.writeToString(doc);
Log(Logger::LOG_INFORMATION) << "***************** Conserved Moiety Converted Document ***************";
Log(Logger::LOG_INFORMATION) << convertedStr;
Log(Logger::LOG_INFORMATION) << "*********************************************************************";
free(convertedStr);
}
}
else
{
doc = ownedDoc;
}
symbols = new LLVMModelDataSymbols(doc->getModel(), options);
modelSymbols = new LLVMModelSymbols(getModel(), *symbols);
// initialize LLVM
// TODO check result
InitializeNativeTarget();
context = new LLVMContext();
// Make the module, which holds all the code.
module = new Module("LLVM Module", *context);
builder = new IRBuilder<>(*context);
// engine take ownership of module
EngineBuilder engineBuilder(module);
engineBuilder.setErrorStr(errString);
executionEngine = engineBuilder.create();
addGlobalMappings();
createLibraryFunctions(module);
ModelDataIRBuilder::createModelDataStructType(module, executionEngine, *symbols);
initFunctionPassManager();
}
catch(const std::exception&)
{
// we might have allocated memory in a failed ctor,
// clean it up here.
// destructors are not called on *this* class when exception is raised
// in the ctor.
cleanup();
throw;
}
}
ModelGeneratorContext::ModelGeneratorContext(std::string const &sbml,
unsigned options) :
ownedDoc(0),
doc(0),
symbols(0),
modelSymbols(0),
errString(new string()),
options(options),
moietyConverter(0),
functionPassManager(0)
{
if (options & rr::ModelGenerator::CONSERVED_MOIETIES)
{
Log(Logger::LOG_NOTICE) << "performing conserved moiety conversion";
moietyConverter = new rr::conservation::ConservedMoietyConverter();
ownedDoc = checkedReadSBMLFromString(sbml.c_str());
if (moietyConverter->setDocument(ownedDoc) != LIBSBML_OPERATION_SUCCESS)
{
throw_llvm_exception("error setting conserved moiety converter document");
}
if (moietyConverter->convert() != LIBSBML_OPERATION_SUCCESS)
{
throw_llvm_exception("error converting document to conserved moieties");
}
doc = moietyConverter->getDocument();
SBMLWriter sw;
char* convertedStr = sw.writeToString(doc);
Log(Logger::LOG_NOTICE) << "***************** Conserved Moiety Converted Document ***************";
Log(Logger::LOG_NOTICE) << convertedStr;
Log(Logger::LOG_NOTICE) << "*********************************************************************";
delete convertedStr;
}
else
{
ownedDoc = checkedReadSBMLFromString(sbml.c_str());
doc = ownedDoc;
}
symbols = new LLVMModelDataSymbols(doc->getModel(), options);
modelSymbols = new LLVMModelSymbols(getModel(), *symbols);
// initialize LLVM
// TODO check result
InitializeNativeTarget();
context = new LLVMContext();
// Make the module, which holds all the code.
module = new Module("LLVM Module", *context);
builder = new IRBuilder<>(*context);
// engine take ownership of module
EngineBuilder engineBuilder(module);
engineBuilder.setErrorStr(errString);
executionEngine = engineBuilder.create();
addGlobalMappings();
createLibraryFunctions(module);
ModelDataIRBuilder::createModelDataStructType(module, executionEngine, *symbols);
initFunctionPassManager();
}
