void CellmlFile::retrieveCmetaIdsFromCellmlElement(iface::cellml_api::CellMLElement *pElement)
{
// Keep track of the given CellML element's cmeta:id
QString cmetaId = QString::fromStdWString(pElement->cmetaId());
if (!cmetaId.isEmpty())
mUsedCmetaIds << cmetaId;
// Do the same for all the child elements of the given CellML element
ObjRef<iface::cellml_api::CellMLElementSet> childElements = pElement->childElements();
ObjRef<iface::cellml_api::CellMLElementIterator> childElementsIter = childElements->iterate();
try {
for (ObjRef<iface::cellml_api::CellMLElement> childElement = childElementsIter->next();
childElement; childElement = childElementsIter->next()) {
retrieveCmetaIdsFromCellmlElement(childElement);
}
} catch (...) {
// Note: we should never reach this point, but it may still happen if a
// CellML file contains a child element that is not known to the
// CellML API. We are taking the view that this is a limitation of
// the CellML API and shouldn't therefore generate an error for
// something that should have been working fine in the first
// place...
}
}
void CellmlFileRuntime::retrieveDaeCodeInformation(iface::cellml_api::Model *pModel)
{
// Get a code generator bootstrap and create a DAE code generator
ObjRef<iface::cellml_services::CodeGeneratorBootstrap> codeGeneratorBootstrap = CreateCodeGeneratorBootstrap();
ObjRef<iface::cellml_services::IDACodeGenerator> codeGenerator = codeGeneratorBootstrap->createIDACodeGenerator();
// Generate some code for the model
try {
mDaeCodeInformation = codeGenerator->generateIDACode(pModel);
// Check that the code generation went fine
checkCodeInformation(mDaeCodeInformation);
} catch (iface::cellml_api::CellMLException &exception) {
couldNotGenerateModelCodeIssue(Core::formatMessage(QString::fromStdWString(exception.explanation)));
} catch (...) {
unknownProblemDuringModelCodeGenerationIssue();
}
// Check the outcome of the DAE code generation
if (mIssues.count())
resetDaeCodeInformation();
}
double SingleCellViewSimulation::requiredMemory()
{
// Determine and return the amount of required memory to run our simulation
// Note #1: we return the amount as a double rather than a qulonglong (as we
// do when retrieving the total/free amount of memory available;
// see [OpenCOR]/src/plugins/misc/Core/src/coreutils.cpp) in case a
// simulation requires an insane amount of memory...
// Note #2: the 1 is for mPoints in SingleCellViewSimulationResults...
iface::cellml_services::CellMLCompiledModel*
compModel(mData->isDAETypeSolver() ?
static_cast<iface::cellml_services::CellMLCompiledModel*>
(mRuntime->daeCompiledModel()) :
static_cast<iface::cellml_services::CellMLCompiledModel*>
(mRuntime->odeCompiledModel()));
ObjRef<iface::cellml_services::CodeInformation> codeInfo
(compModel->codeInformation());
// This is not very accurate at all, because the solver caches a lot more
// information about the problem being solved, some of it bigger than any
// of the below (e.g. Jacobian matricies. Given the solver dependence of
// this size, I'm not sure this function is that useful.
return
size() *
(1 + codeInfo->constantIndexCount() + codeInfo->rateIndexCount() * 3 +
codeInfo->algebraicIndexCount())
* sizeof(double);
}
QStringList CellmlFileRuntime::componentHierarchy(iface::cellml_api::CellMLElement *pElement)
{
// Make sure that we have a given element
if (!pElement)
return QStringList();
// Try to retrieve the component that owns the given element, unless the
// given element is a component itself (which will be the case when we come
// here through recursion)
ObjRef<iface::cellml_api::CellMLComponent> component = QueryInterface(pElement);
ObjRef<iface::cellml_api::CellMLElement> parent = pElement->parentElement();
ObjRef<iface::cellml_api::CellMLComponent> parentComponent = QueryInterface(parent);
if (!component && !parentComponent) {
// The element isn't a component and neither is its parent, so it
// doesn't have a hierarchy
return QStringList();
}
// Recursively retrieve the component hierarchy of the given element's
// encapsulation parent, if any
ObjRef<iface::cellml_api::CellMLComponent> componentEncapsulationParent = component?component->encapsulationParent():parentComponent->encapsulationParent();
return componentHierarchy(componentEncapsulationParent) << QString::fromStdWString(component?component->name():parentComponent->name());
}
//! (static)
std::pair<bool, ObjRef> loadAndExecute(Runtime & runtime, const std::string & filename) {
ObjRef script;
try {
script = loadScriptFile(filename);
} catch (Exception * error) {
std::cerr << "\nError occurred while loading file '" << filename << "':\n" << error->toString() << std::endl;
return std::make_pair(false, error);
}
bool success = true;
ObjRef result;
try {
runtime.executeObj(script.get());
result = runtime.getResult();
if(runtime.getState() == Runtime::STATE_EXCEPTION) {
std::cout << "\nException caught (1):\n" << result.toString() << std::endl;
success = false;
}
} catch (Object * o) {
result = o;
std::cout << "\nException caught (2):\n" << result.toString() << std::endl;
success = false;
} catch (...) {
std::cout << "\nCaught unknown C++ exception." << std::endl;
success = false;
}
return std::make_pair(success, result);
}
QString CellmlFile::xmlBase()
{
// Return the CellML file's base URI
if (load()) {
ObjRef<iface::cellml_api::URI> baseUri = mModel->xmlBase();
return QString::fromStdWString(baseUri->asText());
} else {
return QString();
}
}
bool CellmlFile::load()
{
// Check whether the file is already loaded and without any issues
if (!mLoadingNeeded)
return mIssues.isEmpty();
// Consider the file loaded
// Note: even when we can't load the file, we still consider it 'loaded'
// since we at least tried to load it, so unless the file gets
// modified (and we are to reload it), we are 'fine'...
mLoadingNeeded = false;
// Try to load the model
if (!doLoad(mFileName, QString(), &mModel, mIssues))
return false;
// Retrieve all the RDF triples associated with the model and initialise our
// list of original RDF triples
ObjRef<iface::cellml_api::RDFRepresentation> rdfRepresentation = mModel->getRDFRepresentation(L"http://www.cellml.org/RDF/API");
if (rdfRepresentation) {
mRdfApiRepresentation = QueryInterface(rdfRepresentation);
if (mRdfApiRepresentation) {
mRdfDataSource = mRdfApiRepresentation->source();
ObjRef<iface::rdf_api::TripleSet> rdfTriples = mRdfDataSource->getAllTriples();
ObjRef<iface::rdf_api::TripleEnumerator> rdfTriplesEnumerator = rdfTriples->enumerateTriples();
for (ObjRef<iface::rdf_api::Triple> rdfTriple = rdfTriplesEnumerator->getNextTriple();
rdfTriple; rdfTriple = rdfTriplesEnumerator->getNextTriple()) {
mRdfTriples << new CellmlFileRdfTriple(this, rdfTriple);
}
mRdfTriples.updateOriginalRdfTriples();
}
}
// Determine which cmeta:ids are currently in use, be they in the various
// CellML elements or RDF triples
retrieveCmetaIdsFromCellmlElement(mModel);
foreach (CellmlFileRdfTriple *rdfTriple, mRdfTriples)
mUsedCmetaIds << rdfTriple->metadataId();
mUsedCmetaIds.removeDuplicates();
return true;
}
void SingleCellViewSimulationData::startNextRepeat()
{
mCurrentRepeat++;
if (mCurrentRepeat >= solverProperties()["nrepeats"].toInt()) {
emit simulationComplete();
return;
}
if (mCurrentRepeat == 0)
mStatesWhenRun = mStates;
else
mStates = mStatesWhenRun;
newIntegrationRun();
if (!mIntegrationRun)
return;
mState = SingleCellViewSimulationData::SIMSTATE_WAITING_RESULTS;
iface::cellml_services::CellMLCompiledModel*
compModel(isDAETypeSolver() ?
static_cast<iface::cellml_services::CellMLCompiledModel*>
(mRuntime->daeCompiledModel()) :
static_cast<iface::cellml_services::CellMLCompiledModel*>
(mRuntime->odeCompiledModel()));
ObjRef<iface::cellml_services::CodeInformation> codeInfo
(compModel->codeInformation());
mResultReceiver = new ResultListener(mIntegrationRun, codeInfo->rateIndexCount(),
codeInfo->algebraicIndexCount());
mResultReceiver->delay(mDelay);
mIntegrationRun->setStepSizeControl(mSolverProperties["absTol"].toDouble(),
mSolverProperties["relTol"].toDouble(),
1.0, // Scaling factor: states
1.0, // Scaling factor: rates
mSolverProperties["maxStep"].toDouble());
mIntegrationRun->setResultRange(mStartingPoint, mEndingPoint,
10000.0 // Maximum density of points in bvar, as an upper bound on the number
// of points returned.
);
mIntegrationRun->setProgressObserver(mResultReceiver);
QObject::connect(mResultReceiver, SIGNAL(constantsAvailable(const QList<double>)), this, SIGNAL(constantsAvailable(const QList<double>)));
QObject::connect(mResultReceiver, SIGNAL(solveDone()), this, SLOT(startNextRepeat()));
QObject::connect(mResultReceiver, SIGNAL(solveFailure(QString)), this, SIGNAL(simulationFailed(QString)));
QObject::connect(mResultReceiver, SIGNAL(solvePointAvailable(double,QList<double>,QList<double>,QList<double>)), this, SIGNAL(simulationDataAvailable(double,QList<double>,QList<double>,QList<double>)));
setupOverrides();
mIntegrationRun->start();
}
//! (static)
std::pair<bool, ObjRef> loadAndExecute(Runtime & runtime, const std::string & filename) {
try {
ObjRef result = _loadAndExecute(runtime,filename);
ObjRef exitResult = runtime.fetchAndClearExitResult();
return std::make_pair(true,exitResult.isNotNull() ? exitResult : result);
} catch (Object * error) {
std::ostringstream os;
os << "Error occurred while loading file '" << filename << "':\n" << error->toString() << std::endl;
runtime.log(Logger::LOG_ERROR,os.str());
return std::make_pair(false, error);
}
// }catch(...){
// std::cout << "\nCaught unknown C++ exception." << std::endl;
// return std::make_pair(false, result.detachAndDecrease());
}
bool CellmlFileManager::canLoadFileContents(const QString &pFileContents) const
{
// Try to load the CellML file contents
ObjRef<iface::cellml_api::CellMLBootstrap> cellmlBootstrap = CreateCellMLBootstrap();
ObjRef<iface::cellml_api::DOMModelLoader> modelLoader = cellmlBootstrap->modelLoader();
ObjRef<iface::cellml_api::Model> model;
try {
model = modelLoader->createFromText(pFileContents.toStdWString());
return true;
} catch (iface::cellml_api::CellMLException &) {
return false;
}
}
void
CDA_CellMLElement::addEventListener
(
const std::wstring& aType,
iface::events::EventListener* aListener,
bool aUseCapture
)
throw(std::exception&)
{
// Only bubbling is supported, as these events can't be cancelled.
if (aUseCapture)
throw iface::cellml_api::CellMLException(L"Only bubbling events are supported.");
int32_t event = FindEventByName(aType);
// Unknown events are silently ignored, as per the DOM Events specification.
if (event == -1)
return;
// Find the adaptor, if there is one...
ListenerToAdaptor_t::iterator i = mListenerToAdaptor.find(aListener);
ObjRef<CDA_CellMLElementEventAdaptor> adaptor;
if (i == mListenerToAdaptor.end())
{
// We add a refcount, putting the total to 2...
adaptor = new CDA_CellMLElementEventAdaptor(this, aListener);
// One refcount is used for the map, the other belongs to the ObjRef and
// will be automatically dropped.
mListenerToAdaptor.insert(std::pair<iface::events::EventListener*,
CDA_CellMLElementEventAdaptor*>
(aListener, adaptor)
);
}
else
adaptor = (*i).second;
try
{
adaptor->newEventType(event);
}
catch (std::exception& e)
{
adaptor->considerDestruction();
throw e;
}
}
std::wstring CompactorReport::getReport() const
{
std::wstringstream report;
report << L"Model Compaction Report\n"
<< L"=======================\n\n";
if (! mErrorMessage.empty()) report << L"Error message: " << mErrorMessage << L"\n\n";
std::wstring indent = L"";
if (mVariableForCompaction.size() > 0)
{
report << L"Some variables have not been compacted.\n"
<< L"Uncompacted variables are given below.\n\n";
for (size_t i=0; i<mVariableForCompaction.size(); ++i)
{
ObjRef<iface::cellml_api::CellMLVariable> variable = mVariableForCompaction[i].first;
ObjRef<iface::cellml_api::CellMLVariable> srcVariable = mVariableForCompaction[i].second;
std::wstring modelUri = variable->modelElement()->base_uri()->asText();
std::wstring srcModelUri = srcVariable->modelElement()->base_uri()->asText();
for (size_t j=0;j<i;++j) indent += L"\t";
report << indent << L"Compaction requested for variable: " << modelUri << L" # "
<< variable->componentName() << L" / "
<< variable->name() << L";\n" << indent << L"with the actual source variable being: "
<< srcModelUri << L" # " << srcVariable->componentName() << L" / " << srcVariable->name() << L"\n";
}
}
report.flush();
return report.str();
}
/*! Tries to locate the given __filename__ with the current searchPath set in the runtime.
@return the path to the file or the original __filename__ if the file could not be found. */
static std::string findFile(Runtime & runtime, const std::string & filename){
static const StringId seachPathsId("__searchPaths");
std::string file(IO::condensePath(filename));
if( IO::getEntryType(file)!=IO::TYPE_FILE ){
if(Array * searchPaths = dynamic_cast<Array*>(runtime.getAttribute(seachPathsId).getValue())){
for(ERef<Iterator> itRef=searchPaths->getIterator();!itRef->end();itRef->next()){
ObjRef valueRef = itRef->value();
std::string s(IO::condensePath(valueRef.toString()+'/'+filename));
if( IO::getEntryType(s)==IO::TYPE_FILE ){
file = s;
break;
}
}
}
}
return file;
}
/*! Tries to locate the given __filename__ with the current searchPath set in the runtime.
@return the path to the file or the original __filename__ if the file could not be found. */
static std::string findFile(Runtime & runtime, const std::string & filename){
static const identifierId seachPathsId=stringToIdentifierId("__searchPaths");
std::string file(FileUtils::condensePath(filename));
if( FileUtils::isFile(file)!=1 ){
if(Array * searchPaths = dynamic_cast<Array*>(runtime.getAttribute(seachPathsId))){
for(ERef<Iterator> itRef=searchPaths->getIterator();!itRef->end();itRef->next()){
ObjRef valueRef = itRef->value();
std::string s(FileUtils::condensePath(valueRef.toString()+"/"+filename));
if( FileUtils::isFile(s)==1 ){
file = s;
break;
}
}
}
}
return file;
}
bool CellmlFile::doLoad(const QString &pFileName, const QString &pFileContents,
ObjRef<iface::cellml_api::Model> *pModel,
CellmlFileIssues &pIssues)
{
// Make sure that pIssues is empty
pIssues.clear();
// Get a bootstrap object and its model loader
ObjRef<iface::cellml_api::CellMLBootstrap> cellmlBootstrap = CreateCellMLBootstrap();
ObjRef<iface::cellml_api::DOMModelLoader> modelLoader = cellmlBootstrap->modelLoader();
// Try to create the model
try {
if (pFileContents.isEmpty())
*pModel = modelLoader->loadFromURL(QUrl::fromPercentEncoding(QUrl::fromLocalFile(pFileName).toEncoded()).toStdWString());
else
*pModel = modelLoader->createFromText(pFileContents.toStdWString());
} catch (iface::cellml_api::CellMLException &exception) {
// Something went wrong with the loading of the model
if (pFileContents.isEmpty()) {
pIssues << CellmlFileIssue(CellmlFileIssue::Error,
QObject::tr("the model could not be loaded (%1)").arg(Core::formatMessage(QString::fromStdWString(exception.explanation))));
} else {
pIssues << CellmlFileIssue(CellmlFileIssue::Error,
QObject::tr("the model could not be created (%1)").arg(Core::formatMessage(QString::fromStdWString(exception.explanation))));
}
return false;
}
// Update the base URI, should the CellML file be a remote one or its
// contents be directly passed onto us
Core::FileManager *fileManagerInstance = Core::FileManager::instance();
ObjRef<iface::cellml_api::URI> baseUri = (*pModel)->xmlBase();
if (fileManagerInstance->isRemote(pFileName)) {
// We are dealing with a remote file, so its XML base value should point
// to its remote location
baseUri->asText(fileManagerInstance->url(pFileName).toStdWString());
} else if (!pFileContents.isEmpty()) {
// We are dealing with a file which contents was directly passed onto
// us, so its XML base value should point to its actual location
baseUri->asText(pFileName.toStdWString());
}
return true;
}
bool isCellmlFile(const QString &pFileName)
{
// If the given file is already managed by our CellML file manager, then we
// consider that it's still a CellML file (even though it may not be a
// CellML file anymore after having been edited and saved, but in this case
// it's good to keep considering the file as a CellML file, so that the user
// can continue editing it for example)
QString nativeFileName = Core::nativeCanonicalFileName(pFileName);
if (CellMLSupport::CellmlFileManager::instance()->cellmlFile(nativeFileName))
return true;
// The given file is not managed by our CellML file manager, so check
// whether it's a new file and, if so, consider it as a CellML file
if (Core::FileManager::instance()->isNew(nativeFileName))
return true;
// Check whether we are dealing with an empty file or a file that contains
// spaces of sorts and, if not, whether we can load it using the CellML API
QString fileContents;
if (Core::readTextFromFile(nativeFileName, fileContents)) {
if (fileContents.trimmed().isEmpty())
return true;
ObjRef<iface::cellml_api::CellMLBootstrap> cellmlBootstrap = CreateCellMLBootstrap();
ObjRef<iface::cellml_api::DOMModelLoader> modelLoader = cellmlBootstrap->modelLoader();
ObjRef<iface::cellml_api::Model> model;
try {
model = modelLoader->createFromText(fileContents.toStdWString());
return true;
} catch (iface::cellml_api::CellMLException &) {
return false;
}
} else {
return false;
}
}
Util::GenericAttribute * convertFromEScript(const EScript::ObjPtr & object) override {
// is a Number?
EScript::Number * n = dynamic_cast<EScript::Number *> (object.get());
if (n != nullptr) {
return GenericAttribute::createNumber(n->getValue());
}
// is a Bool?
EScript::Bool * b = dynamic_cast<EScript::Bool *> (object.get());
if (b != nullptr) {
return GenericAttribute::createBool(b->toBool());
}
// is a String?
EScript::String * s = dynamic_cast<EScript::String *> (object.get());
if (s != nullptr) {
return GenericAttribute::createString(s->getString());
}
// is an Array?
EScript::Array * a = dynamic_cast<EScript::Array *> (object.get());
if (a != nullptr) {
auto gl = new Util::GenericAttributeList;
for (ERef<EScript::Iterator> i = a->getIterator(); !i->end(); i->next()) {
ObjRef value = i->value();
gl->push_back(convertEScriptObjectToGenericAttribute(value));
}
return gl;
}
// is a Map?
EScript::Map * m = dynamic_cast<EScript::Map *> (object.get());
if (m != nullptr) {
auto gm = new Util::GenericAttributeMap;
for (ERef<EScript::Iterator> i = m->getIterator(); !i->end(); i->next()) {
ObjRef key = i->key();
ObjRef value = i->value();
gm->setValue(key->toString(), convertEScriptObjectToGenericAttribute(value));
}
return gm;
}
return nullptr;
}
void operator= (const ObjRef<U>& newAssign)
{
T* nap = newAssign.getPointer();
if (mPtr == nap)
return;
if (mPtr)
mPtr->release_ref();
mPtr = nap;
if (mPtr != NULL)
mPtr->add_ref();
}
void SingleCellViewSimulationData::setupOverrides()
{
iface::cellml_services::CellMLCompiledModel*
compModel(isDAETypeSolver() ?
static_cast<iface::cellml_services::CellMLCompiledModel*>
(mRuntime->daeCompiledModel()) :
static_cast<iface::cellml_services::CellMLCompiledModel*>
(mRuntime->odeCompiledModel()));
ObjRef<iface::cellml_services::CodeInformation> codeInfo
(compModel->codeInformation());
for (unsigned int i = 0; i < codeInfo->constantIndexCount(); i++)
if (mInitialConstants[i] != mConstants[i])
mIntegrationRun->setOverride(iface::cellml_services::CONSTANT,
i, mConstants[i]);
for (unsigned int i = 0; i < codeInfo->rateIndexCount(); i++)
if (mInitialStates[i] != mStates[i])
mIntegrationRun->setOverride(iface::cellml_services::STATE_VARIABLE,
i, mStates[i]);
}
int CellmlModelDefinition::loadModelFromString(const std::string &ms)
{
std::cout << "Creating CellML Model Definition from the given model string"
<< std::endl;
mUrl = "";
std::wstring msW = s2ws(ms);
ObjRef<iface::cellml_api::CellMLBootstrap> cb = CreateCellMLBootstrap();
ObjRef<iface::cellml_api::DOMModelLoader> ml = cb->modelLoader();
int code;
try
{
ObjRef<iface::cellml_api::Model> model = ml->createFromText(msW);
model->fullyInstantiateImports();
// we have a model, so we can start grabbing hold of the CellML API objects
mCapi = new CellmlApiObjects();
mCapi->model = model;
code = instantiateCellmlApiObjects();
}
catch (...)
{
std::wcerr << L"Error loading model from string." << std::endl;
return -1;
}
return code;
}
int CellmlModelDefinition::loadModel(const std::string &url)
{
std::cout << "Creating CellML Model Definition from the URL: "
<< url << std::endl;
mUrl = url;
if (mUrl.empty()) return -1;
std::wstring urlW = s2ws(url);
ObjRef<iface::cellml_api::CellMLBootstrap> cb = CreateCellMLBootstrap();
ObjRef<iface::cellml_api::DOMModelLoader> ml = cb->modelLoader();
int code;
try
{
ObjRef<iface::cellml_api::Model> model = ml->loadFromURL(urlW);
model->fullyInstantiateImports();
// we have a model, so we can start grabbing hold of the CellML API objects
mCapi = new CellmlApiObjects();
mCapi->model = model;
code = instantiateCellmlApiObjects();
}
catch (...)
{
std::wcerr << L"Error loading model: " << urlW << std::endl;
return -1;
}
return code;
}
//! ---|> [Object]
Object * ForeachControl::execute(Runtime & rt) {
ERef<Iterator> itRef=dynamic_cast<Iterator *>(rt.executeObj(arrayExpressionRef.get()));
if(!rt.assertNormalState(this) || itRef.isNull())
return NULL;
ObjRef resultRef;
while (!itRef->end()) {
if (keyVar)
rt.assignToVariable(keyVar,itRef->key());
if (valueVar)
rt.assignToVariable(valueVar,itRef->value());
if(!actionRef.isNull()){
try {
resultRef=rt.executeObj(actionRef.get());
} catch (Object * e) {
std::cout << "###"<<e<<itRef->key();
throw(e);
}
if(!rt.checkNormalState()){
if(rt.getState()==Runtime::STATE_BREAKING){
rt.resetState();
break;
}else if(rt.getState()==Runtime::STATE_CONTINUE){
rt.resetState();
}else{
return NULL;
}
}
}
itRef->next();
}
return resultRef.detachAndDecrease();
}
ObjRef<iface::cellml_api::CellMLVariable> findLocalVariable(CellmlApiObjects* capi, const std::string& variableId)
{
if (!(capi->cevas))
{
std::cerr << "CellMLModelDefinition::findLocalVariable -- missing CeVAS object?" << std::endl;
return NULL;
}
// find named variable - in local components only!
CVpair cv = splitName(variableId);
if ((cv.first.length() == 0) || (cv.second.length() == 0)) return NULL;
//std::cout << "Component name: " << cv.first << "; variable name: " << cv.second << std::endl;
ObjRef<iface::cellml_api::CellMLComponentSet> components = capi->model->localComponents();
ObjRef<iface::cellml_api::CellMLComponent> component = components->getComponent(s2ws(cv.first));
if (!component)
{
std::cerr << "CellMLModelDefinition::findLocalVariable -- unable to find local component: " << cv.first << std::endl;
return NULL;
}
ObjRef<iface::cellml_api::CellMLVariableSet> variables = component->variables();
ObjRef<iface::cellml_api::CellMLVariable> variable = variables->getVariable(s2ws(cv.second));
if (!variable)
{
std::cerr << "CellMLModelDefinition::findLocalVariable -- unable to find variable: " << cv.first << " / "
<< cv.second << std::endl;
return NULL;
}
// get source variable
ObjRef<iface::cellml_services::ConnectedVariableSet> cvs = capi->cevas->findVariableSet(variable);
ObjRef<iface::cellml_api::CellMLVariable> v = cvs->sourceVariable();
if (!v)
{
std::cerr << "CellMLModelDefinition::findLocalVariable -- unable get source variable for variable: "
<< cv.first << " / " << cv.second << std::endl;
return NULL;
}
return v;
}
CellmlFileRdfTripleElement::CellmlFileRdfTripleElement(iface::rdf_api::Node *pRdfNode) :
mId(QString()),
mUriReference(QString()),
mLexicalForm(QString()),
mLanguage(QString()),
mDataTypeUri(QString())
{
// Check which interface is supported by the node and initialise it in case
// it supports the rdf_api::URIReference, rdf_api::PlainLiteral or
// rdf_api::TypedLiteral interface
ObjRef<iface::rdf_api::URIReference> uriReference = QueryInterface(pRdfNode);
if (uriReference) {
// The rdf_api::URIReference interface is supported, so initialise the
// triple element using that interface
mType = UriReference;
mUriReference = QString::fromStdWString(uriReference->URI()).trimmed();
} else {
ObjRef<iface::rdf_api::PlainLiteral> plainLiteral = QueryInterface(pRdfNode);
if (plainLiteral) {
// The rdf_api::PlainLiteral interface is supported, so initialise
// the triple element using that interface
mType = PlainLiteral;
mLexicalForm = QString::fromStdWString(plainLiteral->lexicalForm()).trimmed();
mLanguage = QString::fromStdWString(plainLiteral->language()).trimmed();
} else {
ObjRef<iface::rdf_api::TypedLiteral> typedLiteral = QueryInterface(pRdfNode);
if (typedLiteral) {
// The rdf_api::TypedLiteral interface is supported, so
// initialise the triple element using that interface
mType = TypedLiteral;
mLexicalForm = QString::fromStdWString(typedLiteral->lexicalForm()).trimmed();
mDataTypeUri = QString::fromStdWString(typedLiteral->datatypeURI()).trimmed();
} else {
// The node doesn't support any interface, so initialise the
// triple element using its id
// Note: the id returned by the CellML API will look something
// like
//
// 7EQ?;?Y?A?w???A
//
// This is clearly not user-friendly, so we generate and
// use our own id instead...
static QMap<QString, QString> ids;
static int counter = 0;
QString id = QString::fromStdString(pRdfNode->objid()).trimmed();
mType = Id;
mId = ids.value(id);
if (mId == QString()) {
// There is no id value for the current id, so generate one
// and keep track of it
mId = QString("id_%1").arg(++counter, 9, 10, QChar('0'));
ids.insert(id, mId);
}
}
}
}
// Keep track of the RDF triple element's value as a string, which is based
// on its type
switch (mType) {
case UriReference:
mAsString = mUriReference;
break;
case PlainLiteral:
mAsString = mLexicalForm+" ["+mLanguage+"]";
break;
case TypedLiteral:
mAsString = mLexicalForm+" ["+mDataTypeUri+"]";
break;
default:
// Id
mAsString = mId;
}
}
void
WriteCode(iface::cellml_services::CodeInformation* cci, uint32_t useida)
{
iface::cellml_services::ModelConstraintLevel mcl =
cci->constraintLevel();
if (mcl == iface::cellml_services::UNDERCONSTRAINED)
{
ObjRef<iface::cellml_services::ComputationTarget> ctMissingIV(cci->missingInitial());
if (ctMissingIV != NULL)
{
ObjRef<iface::cellml_api::CellMLVariable> v = ctMissingIV->variable();
std::wstring n = v->name();
std::wstring c = v->componentName();
std::wstring str;
uint32_t deg = ctMissingIV->degree();
if (deg != 0)
{
str += L"d^";
wchar_t buf[20];
any_swprintf(buf, 20, L"%u", deg);
str += buf;
str += L"/dt^";
str += buf;
str += L" ";
}
str += n;
str += L" (in ";
str += c;
str += L")\n";
printf("/* Model is underconstrained due to missing initial_value on %S\n", str.c_str());
}
else
{
printf("/* Model is underconstrained.\n"
" * List of undefined targets follows...\n");
iface::cellml_services::ComputationTargetIterator* cti = cci->iterateTargets();
iface::cellml_services::ComputationTarget* ct;
std::vector<std::wstring> messages;
while (true)
{
ct = cti->nextComputationTarget();
if (ct == NULL)
break;
if (ct->type() != iface::cellml_services::FLOATING)
{
ct->release_ref();
continue;
}
iface::cellml_api::CellMLVariable* v = ct->variable();
std::wstring n = v->name();
std::wstring c = v->componentName();
std::wstring str = L" * * ";
uint32_t deg = ct->degree();
if (deg != 0)
{
str += L"d^";
wchar_t buf[20];
any_swprintf(buf, 20, L"%u", deg);
str += buf;
str += L"/dt^";
str += buf;
str += L" ";
}
str += n;
str += L" (in ";
str += c;
str += L")\n";
messages.push_back(str);
v->release_ref();
ct->release_ref();
}
cti->release_ref();
// Sort the messages...
std::sort(messages.begin(), messages.end());
std::vector<std::wstring>::iterator msgi;
for (msgi = messages.begin(); msgi != messages.end(); msgi++)
printf("%S", (*msgi).c_str());
printf(" */\n");
}
return;
}
else if (mcl == iface::cellml_services::OVERCONSTRAINED)
{
printf("/* Model is overconstrained.\n"
" * List variables defined at time of error follows...\n");
iface::cellml_services::ComputationTargetIterator* cti = cci->iterateTargets();
iface::cellml_services::ComputationTarget* ct;
std::vector<std::wstring> messages;
while (true)
{
ct = cti->nextComputationTarget();
if (ct == NULL)
break;
if (ct->type() == iface::cellml_services::FLOATING)
{
ct->release_ref();
continue;
}
iface::cellml_api::CellMLVariable* v = ct->variable();
std::wstring n = v->name();
std::wstring str = L" * * ";
uint32_t deg = ct->degree();
if (deg != 0)
{
str += L"d^";
wchar_t buf[20];
any_swprintf(buf, 20, L"%u", deg);
str += buf;
str += L"/dt^";
str += buf;
str += L" ";
}
str += n;
str += L"\n";
messages.push_back(str);
v->release_ref();
ct->release_ref();
}
cti->release_ref();
// Sort the messages...
std::sort(messages.begin(), messages.end());
std::vector<std::wstring>::iterator msgi;
for (msgi = messages.begin(); msgi != messages.end(); msgi++)
printf("%S", (*msgi).c_str());
// Get flagged equations...
iface::mathml_dom::MathMLNodeList* mnl = cci->flaggedEquations();
printf(" * Extraneous equation was:\n");
iface::dom::Node* n = mnl->item(0);
mnl->release_ref();
iface::dom::Element* el =
reinterpret_cast<iface::dom::Element*>(n->query_interface("dom::Element"));
n->release_ref();
std::wstring cmeta = el->getAttribute(L"id");
if (cmeta == L"")
printf(" * <equation with no cmeta ID>\n");
else
printf(" * %S\n", cmeta.c_str());
n = el->parentNode();
el->release_ref();
if (n != NULL)
{
el = reinterpret_cast<iface::dom::Element*>
(n->query_interface("dom::Element"));
n->release_ref();
cmeta = el->getAttribute(L"id");
if (cmeta == L"")
printf(" * in <math with no cmeta ID>\n");
else
printf(" * in math with cmeta:id %S\n", cmeta.c_str());
el->release_ref();
}
printf(" */\n");
return;
}
else if (mcl == iface::cellml_services::UNSUITABLY_CONSTRAINED)
{
printf("/* Model is unsuitably constrained (i.e. would need capabilities"
" beyond those of the CCGS to solve).\n"
" * The status of variables at time of error follows...\n");
iface::cellml_services::ComputationTargetIterator* cti = cci->iterateTargets();
iface::cellml_services::ComputationTarget* ct;
std::vector<std::wstring> messages;
while (true)
{
ct = cti->nextComputationTarget();
if (ct == NULL)
break;
std::wstring str = L" * * ";
if (ct->type() == iface::cellml_services::FLOATING)
str += L" Undefined: ";
else
str += L" Defined: ";
uint32_t deg = ct->degree();
if (deg != 0)
{
str += L"d^";
wchar_t buf[20];
any_swprintf(buf, 20, L"%u", deg);
str += buf;
str += L"/dt^";
str += buf;
str += L" ";
}
iface::cellml_api::CellMLVariable* v = ct->variable();
std::wstring n = v->name();
str += n;
str += L"\n";
messages.push_back(str);
v->release_ref();
ct->release_ref();
}
cti->release_ref();
// Sort the messages...
std::sort(messages.begin(), messages.end());
std::vector<std::wstring>::iterator msgi;
for (msgi = messages.begin(); msgi != messages.end(); msgi++)
printf("%S", (*msgi).c_str());
printf(" */\n");
return;
}
printf("/* Model is correctly constrained.\n");
iface::mathml_dom::MathMLNodeList* mnl = cci->flaggedEquations();
uint32_t i, l = mnl->length();
if (l == 0)
printf(" * No equations needed Newton-Raphson evaluation.\n");
else
printf(" * The following equations needed Newton-Raphson evaluation:\n");
std::vector<std::wstring> messages;
for (i = 0; i < l; i++)
{
iface::dom::Node* n = mnl->item(i);
iface::dom::Element* el =
reinterpret_cast<iface::dom::Element*>(n->query_interface("dom::Element"));
n->release_ref();
std::wstring cmeta = el->getAttribute(L"id");
std::wstring str;
if (cmeta == L"")
str += L" * <equation with no cmeta ID>\n";
else
{
str += L" * ";
str += cmeta;
str += L"\n";
}
n = el->parentNode();
el->release_ref();
el = reinterpret_cast<iface::dom::Element*>
(n->query_interface("dom::Element"));
n->release_ref();
cmeta = el->getAttribute(L"id");
if (cmeta == L"")
str += L" * in <math with no cmeta ID>\n";
else
{
str += L" * in math with cmeta:id ";
str += cmeta;
str += L"\n";
}
el->release_ref();
messages.push_back(str);
}
mnl->release_ref();
// Sort the messages...
std::sort(messages.begin(), messages.end());
std::vector<std::wstring>::iterator msgi;
for (msgi = messages.begin(); msgi != messages.end(); msgi++)
printf("%S", (*msgi).c_str());
printf(" * The rate and state arrays need %u entries.\n", cci->rateIndexCount());
printf(" * The algebraic variables array needs %u entries.\n", cci->algebraicIndexCount());
printf(" * The constant array needs %u entries.\n", cci->constantIndexCount());
printf(" * Variable storage is as follows:\n");
messages.clear();
iface::cellml_services::ComputationTargetIterator* cti = cci->iterateTargets();
while (true)
{
iface::cellml_services::ComputationTarget* ct = cti->nextComputationTarget();
if (ct == NULL)
break;
iface::cellml_api::CellMLVariable* v = ct->variable();
iface::cellml_api::CellMLElement* el = v->parentElement();
iface::cellml_api::CellMLComponent* c =
reinterpret_cast<iface::cellml_api::CellMLComponent*>
(el->query_interface("cellml_api::CellMLComponent"));
el->release_ref();
std::wstring str;
std::wstring vn = v->name(), cn = c->name();
str += L" * * Target ";
uint32_t deg = ct->degree();
if (deg != 0)
{
str += L"d^";
wchar_t buf[20];
any_swprintf(buf, 20, L"%u", deg);
str += buf;
str += L"/dt^";
str += buf;
str += L" ";
}
str += vn;
str += L" in component ";
str += cn;
str += L"\n";
c->release_ref();
v->release_ref();
str += L" * * * Variable type: ";
str += TypeToString(ct->type());
str += L"\n * * * Variable index: ";
wchar_t buf[40];
any_swprintf(buf, 40, L"%u\n", ct->assignedIndex());
str += buf;
str += L" * * * Variable storage: ";
std::wstring vsn = ct->name();
str += vsn;
str += '\n';
ct->release_ref();
messages.push_back(str);
}
cti->release_ref();
// Sort the messages...
std::sort(messages.begin(), messages.end());
for (msgi = messages.begin(); msgi != messages.end(); msgi++)
printf("%S", (*msgi).c_str());
printf(" */\n");
std::wstring frag = cci->functionsString();
printf("%S", frag.c_str());
// Now start the code...
frag = cci->initConstsString();
printf("void SetupFixedConstants(double* CONSTANTS, double* RATES, double* STATES)\n{\n%S}\n", frag.c_str());
frag = cci->variablesString();
printf("void EvaluateVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)\n"
"{\n%S}\n", frag.c_str());
if (useida)
{
iface::cellml_services::IDACodeInformation* icci
= reinterpret_cast<iface::cellml_services::IDACodeInformation*>(cci->query_interface("cellml_services::IDACodeInformation"));
frag = icci->essentialVariablesString();
printf("void EvaluateEssentialVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)\n"
"{\n%S}\n", frag.c_str());
frag = cci->ratesString();
printf("void ComputeResiduals(double VOI, double* STATES, double* RATES, double* CONSTANTS, "
"double* ALGEBRAIC)\n"
"{\n%S}\n", frag.c_str());
frag = icci->stateInformationString();
printf("void SetupStateInfo(double * SI)\n{\n%S}\n", frag.c_str());
frag = icci->rootInformationString();
printf("void RootInformation()\n{\n%S}\n", frag.c_str());
icci->release_ref();
}
else
{
frag = cci->ratesString();
printf("void ComputeRates(double VOI, double* STATES, double* RATES, double* CONSTANTS, "
"double* ALGEBRAIC)\n"
"{\n%S}\n", frag.c_str());
}
}
int main(int argc, char** argv)
{
try
{
std::wstring modelURL
(L"http://models.cellml.org/workspace/hodgkin_huxley_1952/@@rawfile/949cd4d3/hodgkin_huxley_1952.cellml");
// Create a CellML Bootstrap and a model loader.
ObjRef<iface::cellml_api::CellMLBootstrap> bootstrap(CreateCellMLBootstrap());
ObjRef<iface::cellml_api::DOMModelLoader> loader(bootstrap->modelLoader());
// Load a CellML model.
ObjRef<iface::cellml_api::Model> hhModel
(loader->loadFromURL(modelURL));
// Request a RDF/API capable RDF representation...
ObjRef<iface::cellml_api::RDFRepresentation> rr(hhModel->getRDFRepresentation(L"http://www.cellml.org/RDF/API"));
ObjRef<iface::rdf_api::RDFAPIRepresentation> rrHH(QueryInterface(rr));
// Retrieve the DataSource. Note: Changes to the data source are not pushed back
// to the model until the source attribute is set on the rrHH again.
ObjRef<iface::rdf_api::DataSource> dsHH(rrHH->source());
// Get the resource corresponding to the cmeta:id on the model. Note that
// cmetaId can return the empty string, which you should check for in
// production code, if there is no cmeta:id
ObjRef<iface::rdf_api::URIReference> hhModelRef
(dsHH->getURIReference(bootstrap->makeURLAbsolute(modelURL, L"#" + hhModel->cmetaId())));
#ifdef DUMP_ALL_TRIPLES_FIRST
{
ObjRef<iface::rdf_api::TripleSet> ts(dsHH->getAllTriples());
ObjRef<iface::rdf_api::TripleEnumerator> te(ts->enumerateTriples());
while (true)
{
ObjRef<iface::rdf_api::Triple> t(te->getNextTriple());
if (t == NULL)
break;
displayTriple(t);
}
}
#endif
ObjRef<iface::rdf_api::URIReference> pmid(dsHH->getURIReference(L"http://www.cellml.org/bqs/1.0#Pubmed_id"));
// Note: Calls like this could fail with an exception if there was no pubmed ID - production code should check.
ObjRef<iface::rdf_api::Triple> t(hhModelRef->getTripleOutOfByPredicate(pmid));
ObjRef<iface::rdf_api::Node> n(t->object());
ObjRef<iface::rdf_api::Literal> lPMID(QueryInterface(n));
if (lPMID != NULL) // It will be null if for some reason it isn't a literal...
std::wcout << L"Model pubmed ID: " << lPMID->lexicalForm() << std::endl;
ObjRef<iface::rdf_api::URIReference> bqsReference(dsHH->getURIReference(L"http://www.cellml.org/bqs/1.0#reference"));
ObjRef<iface::rdf_api::TripleSet> ts(hhModelRef->getTriplesOutOfByPredicate(bqsReference));
ObjRef<iface::rdf_api::TripleEnumerator> te(ts->enumerateTriples());
while (true)
{
t = te->getNextTriple();
if (t == NULL) break;
ObjRef<iface::rdf_api::Resource> r(QueryInterface(t->object()));
if (r == NULL) continue;
std::wcout << L"Found a resource description:" << std::endl;
try
{
t = r->getTripleOutOfByPredicate(pmid);
n = t->object();
lPMID = QueryInterface(n);
if (lPMID != NULL)
std::wcout << L" Reference pubmed ID: " << lPMID->lexicalForm() << std::endl;
}
catch(...) {}
// Look up the subject...
ObjRef<iface::rdf_api::URIReference> subject(dsHH->getURIReference(L"http://purl.org/dc/elements/1.1/subject"));
ts = r->getTriplesOutOfByPredicate(subject);
ObjRef<iface::rdf_api::TripleEnumerator> te2 = ts->enumerateTriples();
while (true)
{
t = te2->getNextTriple();
if (t == NULL)
break;
n = t->object();
r = QueryInterface(n);
if (r == NULL)
continue;
std::wcout << " Subject:" << std::endl;
ObjRef<iface::rdf_api::URIReference> subjectType(dsHH->getURIReference(L"http://www.cellml.org/bqs/1.0#subject_type"));
ts = r->getTriplesOutOfByPredicate(subjectType);
ObjRef<iface::rdf_api::TripleEnumerator> te3 = ts->enumerateTriples();
t = te3->getNextTriple();
if (t)
{
n = t->object();
ObjRef<iface::rdf_api::Literal> l(QueryInterface(n));
std::wcout << " Subject Type=" << l->lexicalForm() << std::endl;
}
ObjRef<iface::rdf_api::URIReference> value(dsHH->getURIReference(L"http://www.w3.org/1999/02/22-rdf-syntax-ns#value"));
ts = r->getTriplesOutOfByPredicate(value);
te3 = ts->enumerateTriples();
t = te3->getNextTriple();
if (t == NULL) continue;
n = t->object();
r = QueryInterface(n);
if (r == NULL) continue;
ObjRef<iface::rdf_api::Container> cont(r->correspondingContainer());
// Add a new entry to the container first...
ObjRef<iface::rdf_api::PlainLiteral> newPL(dsHH->getPlainLiteral(L"Newly created label", L"en"));
cont->appendChild(newPL);
// Delete any labels that match 'giant axon'...
ObjRef<iface::rdf_api::NodeIterator> ni(cont->iterateChildren());
while (true)
{
ObjRef<iface::rdf_api::Node> n(ni->getNextNode());
if (n == NULL)
break;
ObjRef<iface::rdf_api::Literal> l(QueryInterface(n));
if (l == NULL)
continue;
if (l->lexicalForm() == L"giant axon")
// The false means don't renumber immediately. This leaves the
// container with gaps...
cont->removeChild(l, false);
}
cont->renumberContainer(); // Remove the gaps.
displayContainer(cont, L" ");
}
}
}
catch (iface::cellml_api::CellMLException&)
{
std::wcout << L"A CellMLException was raised. In production code, you would normally have more "
<< L"exception handlers to work out exactly where the problem occurred. This program "
<< L"avoids that for simplicity, to make the normal control flow easier to understand. "
<< L"The most likely cause is a network problem retrieving the hardcoded model URL."
<< std::endl;
return 1;
}
catch (iface::rdf_api::RDFProcessingError&)
{
std::wcout << L"An RDFProcessingError was raised. In production code, you would normally have more "
<< L"exception handlers to work out exactly where the problem occurred. This program "
<< L"avoids that for simplicity, to make the normal control flow easier to understand."
<< std::endl;
return 2;
}
return 0;
}
void CellmlFileRuntime::update()
{
// Reset the runtime's properties
reset(true, true);
// Check that the model is either a 'simple' ODE model or a DAE model
// Note #1: we don't check whether a model is valid, since all we want is to
// update its runtime (which has nothing to do with editing or even
// validating a model), so if it can be done then great otherwise
// tough luck (so to speak)...
// Note #2: in order to do so, we need to get a 'normal' code generator (as
// opposed to an IDA, i.e. DAE, code generator) since if the model
// is correctly constrained, then we can check whether some of its
// equations were flagged as needing a Newton-Raphson evaluation,
// in which case we would be dealing with a DAE model...
// Note #3: ideally, there would be a more convenient way to determine the
// type of a model, but there isn't...
iface::cellml_api::Model *model = mCellmlFile->model();
if (!model)
return;
// Retrieve the model's type
// Note: this can be done by checking whether some equations were flagged
// as needing a Newton-Raphson evaluation...
retrieveOdeCodeInformation(model);
if (!mOdeCodeInformation)
return;
ObjRef<iface::mathml_dom::MathMLNodeList> flaggedEquations = mOdeCodeInformation->flaggedEquations();
mModelType = flaggedEquations->length()?CellmlFileRuntime::Dae:CellmlFileRuntime::Ode;
// If the model is of DAE type, then we don't want the ODE-specific code
// information, but the DAE-specific code one
ObjRef<iface::cellml_services::CodeInformation> genericCodeInformation;
if (mModelType == CellmlFileRuntime::Ode) {
genericCodeInformation = mOdeCodeInformation;
} else {
retrieveDaeCodeInformation(model);
if (!mDaeCodeInformation)
return;
genericCodeInformation = mDaeCodeInformation;
}
// Retrieve the number of constants, states/rates, algebraic and conditional
// variables in the model
// Note: this is to avoid having to go through the ODE/DAE code information
// an unnecessary number of times when we want to retrieve either of
// those numbers (e.g. see
// SingleCellViewSimulationResults::addPoint())...
if (mModelType == CellmlFileRuntime::Ode) {
mConstantsCount = mOdeCodeInformation->constantIndexCount();
mStatesRatesCount = mOdeCodeInformation->rateIndexCount();
mAlgebraicCount = mOdeCodeInformation->algebraicIndexCount();
mCondVarCount = 0;
} else {
mConstantsCount = mDaeCodeInformation->constantIndexCount();
mStatesRatesCount = mDaeCodeInformation->rateIndexCount();
mAlgebraicCount = mDaeCodeInformation->algebraicIndexCount();
mCondVarCount = mDaeCodeInformation->conditionVariableCount();
}
// Determine whether the model imports some components
// Note #1: a model that only imports units will clearly not affect our
// model's variables, hence such a model won't be relevant for our
// mapping below...
// Note #2: a model cannot be fully instantiated if it imports an empty
// component or a component with unmapped variables, so we don't
// need to worry about this type of model...
ObjRef<iface::cellml_api::CellMLImportSet> imports = model->imports();
ObjRef<iface::cellml_api::CellMLImportIterator> importsIter = imports->iterateImports();
bool hasComponentImports = false;
for (ObjRef<iface::cellml_api::CellMLImport> import = importsIter->nextImport();
import; import = importsIter->nextImport()) {
ObjRef<iface::cellml_api::ImportComponentSet> importComponents = import->components();
if (importComponents->length()) {
hasComponentImports = true;
break;
}
}
// If the model contains some imports then we want to to go through the
// variables defined or referenced in our main CellML file and do a mapping
// between the source of a variable and a variable in the main CellML file
// Note: indeed, when it comes to CellML 1.1 files, we only want to list the
// parameters that are either defined or referenced in our main CellML
// file. Not only does it make sense, but also only the parameters
// listed in a main CellML file can be referenced in SED-ML...
QMap<iface::cellml_api::CellMLVariable *, iface::cellml_api::CellMLVariable *> mainVariables = QMap<iface::cellml_api::CellMLVariable *, iface::cellml_api::CellMLVariable *>();
ObjRef<iface::cellml_api::CellMLComponentSet> localComponents = model->localComponents();
ObjRef<iface::cellml_api::CellMLComponentIterator> localComponentsIter = localComponents->iterateComponents();
if (hasComponentImports) {
for (ObjRef<iface::cellml_api::CellMLComponent> component = localComponentsIter->nextComponent();
component; component = localComponentsIter->nextComponent()) {
ObjRef<iface::cellml_api::CellMLVariableSet> variables = component->variables();
ObjRef<iface::cellml_api::CellMLVariableIterator> variablesIter = variables->iterateVariables();
for (ObjRef<iface::cellml_api::CellMLVariable> variable = variablesIter->nextVariable();
variable; variable = variablesIter->nextVariable()) {
ObjRef<iface::cellml_api::CellMLVariable> sourceVariable = variable->sourceVariable();
mainVariables.insert(sourceVariable, variable);
}
}
}
// Go through all our computation targets and determine which ones are
// referenced in our main CellML file, and sort them by component and
// variable name
ObjRef<iface::cellml_services::ComputationTargetIterator> computationTargetIter = genericCodeInformation->iterateTargets();
for (ObjRef<iface::cellml_services::ComputationTarget> computationTarget = computationTargetIter->nextComputationTarget();
computationTarget; computationTarget = computationTargetIter->nextComputationTarget()) {
// Make sure that our computation target is defined or referenced in our
// main CellML file, if it has imports
ObjRef<iface::cellml_api::CellMLVariable> variable = computationTarget->variable();
iface::cellml_api::CellMLVariable *mainVariable = mainVariables.value(variable);
iface::cellml_api::CellMLVariable *realVariable = mainVariable?mainVariable:variable.getPointer();
if ( hasComponentImports && !mainVariable
&& (computationTarget->type() != iface::cellml_services::VARIABLE_OF_INTEGRATION)) {
continue;
}
// Determine the type of our computation target
CellmlFileRuntimeParameter::ParameterType parameterType;
switch (computationTarget->type()) {
case iface::cellml_services::VARIABLE_OF_INTEGRATION:
parameterType = CellmlFileRuntimeParameter::Voi;
break;
case iface::cellml_services::CONSTANT:
// We are dealing with a constant, but the question is whether that
// constant is a 'proper' constant, a 'computed' constant or even a
// rate, and this can be determined by checking whether the computed
// target has an initial value or even a degree
// Note: a state variable that is initialised using the initial
// value of another variable will have its rate considered as
// a constant. However, when it comes to the GUI, we really
// want it to be seen as a rate hence we check for the degree
// of the computed target...
if (QString::fromStdWString(variable->initialValue()).isEmpty()) {
// The computed target doesn't have an initial value, so it must
// be a 'computed' constant
parameterType = CellmlFileRuntimeParameter::ComputedConstant;
} else if (computationTarget->degree()) {
// The computed target has a degree, so it is effectively a rate
parameterType = CellmlFileRuntimeParameter::Rate;
} else {
// The computed target has an initial value, so it must be a
// 'proper' constant
parameterType = CellmlFileRuntimeParameter::Constant;
}
break;
case iface::cellml_services::STATE_VARIABLE:
case iface::cellml_services::PSEUDOSTATE_VARIABLE:
parameterType = CellmlFileRuntimeParameter::State;
break;
case iface::cellml_services::ALGEBRAIC:
// We are dealing with either a 'proper' algebraic variable or a
// rate variable
// Note: if the variable's degree is equal to zero, then we are
// dealing with a 'proper' algebraic variable otherwise we
// are dealing with a rate variable...
if (computationTarget->degree())
parameterType = CellmlFileRuntimeParameter::Rate;
else
parameterType = CellmlFileRuntimeParameter::Algebraic;
break;
case iface::cellml_services::FLOATING:
parameterType = CellmlFileRuntimeParameter::Floating;
break;
case iface::cellml_services::LOCALLY_BOUND:
parameterType = CellmlFileRuntimeParameter::LocallyBound;
break;
}
// Keep track of our computation target, should its type be of interest
if ( (parameterType != CellmlFileRuntimeParameter::Floating)
&& (parameterType != CellmlFileRuntimeParameter::LocallyBound)) {
CellmlFileRuntimeParameter *parameter = new CellmlFileRuntimeParameter(QString::fromStdWString(realVariable->name()),
computationTarget->degree(),
QString::fromStdWString(realVariable->unitsName()),
componentHierarchy(realVariable),
parameterType,
computationTarget->assignedIndex());
if (parameterType == CellmlFileRuntimeParameter::Voi)
mVariableOfIntegration = parameter;
if (!hasComponentImports || (realVariable == mainVariable))
mParameters << parameter;
}
}
std::sort(mParameters.begin(), mParameters.end(), sortParameters);
// Generate the model code
QString modelCode = QString();
QString functionsString = QString::fromStdWString(genericCodeInformation->functionsString());
if (!functionsString.isEmpty()) {
// We will need to solve at least one NLA system
mAtLeastOneNlaSystem = true;
modelCode += "struct rootfind_info\n"
"{\n"
" double aVOI;\n"
"\n"
" double *aCONSTANTS;\n"
" double *aRATES;\n"
" double *aSTATES;\n"
" double *aALGEBRAIC;\n"
"\n"
" int *aPRET;\n"
"};\n"
"\n"
"extern void doNonLinearSolve(char *, void (*)(double *, double *, void*), double *, int *, int, void *);\n"
"\n"
+functionsString.replace("do_nonlinearsolve(", QString("doNonLinearSolve(\"%1\", ").arg(address()))
+"\n";
// Note: we rename do_nonlinearsolve() to doNonLinearSolve() because
// CellML's CIS service already defines do_nonlinearsolve(), yet
// we want to use our own non-linear solve routine defined in our
// Compiler plugin. Also, we add a new parameter to all our calls
// to doNonLinearSolve() so that doNonLinearSolve() can retrieve
// the correct instance of our NLA solver...
}
// Retrieve the body of the function that initialises constants and extract
// the statements that are related to computed variables (since we want to
// be able to recompute those whenever the user modifies a parameter)
// Note: ideally, we wouldn't have to do that, but the CellML API doesn't
// distinguish between 'proper' and 'computed' constants...
// (See https://tracker.physiomeproject.org/show_bug.cgi?id=3499)
static const QRegularExpression InitializationStatementRegEx = QRegularExpression("^(CONSTANTS|RATES|STATES)\\[\\d*\\] = [+-]?\\d*\\.?\\d+([eE][+-]?\\d+)?;$");
QStringList initConstsList = cleanCode(genericCodeInformation->initConstsString()).split("\n");
QString initConsts = QString();
QString compCompConsts = QString();
foreach (const QString &initConst, initConstsList) {
// Add the statement either to our list of 'proper' constants or
// 'computed' constants
if (InitializationStatementRegEx.match(initConst).hasMatch())
initConsts += (initConsts.isEmpty()?QString():"\n")+initConst;
else
compCompConsts += (compCompConsts.isEmpty()?QString():"\n")+initConst;
}
modelCode += functionCode("int initializeConstants(double *CONSTANTS, double *RATES, double *STATES)",
initConsts, true);
modelCode += "\n";
modelCode += functionCode("int computeComputedConstants(double *CONSTANTS, double *RATES, double *STATES)",
compCompConsts, true);
modelCode += "\n";
// Retrieve the body of the remaining functions
if (mModelType == CellmlFileRuntime::Ode) {
modelCode += functionCode("int computeOdeRates(double VOI, double *CONSTANTS, double *RATES, double *STATES, double *ALGEBRAIC)",
cleanCode(mOdeCodeInformation->ratesString()));
modelCode += "\n";
modelCode += functionCode("int computeOdeVariables(double VOI, double *CONSTANTS, double *RATES, double *STATES, double *ALGEBRAIC)",
cleanCode(genericCodeInformation->variablesString()));
} else {
modelCode += functionCode("int computeDaeEssentialVariables(double VOI, double *CONSTANTS, double *RATES, double *OLDRATES, double *STATES, double *OLDSTATES, double *ALGEBRAIC, double *CONDVAR)",
cleanCode(mDaeCodeInformation->essentialVariablesString()));
modelCode += "\n";
modelCode += functionCode("int computeDaeResiduals(double VOI, double *CONSTANTS, double *RATES, double *OLDRATES, double *STATES, double *OLDSTATES, double *ALGEBRAIC, double *CONDVAR, double *resid)",
cleanCode(mDaeCodeInformation->ratesString()));
modelCode += "\n";
modelCode += functionCode("int computeDaeRootInformation(double VOI, double *CONSTANTS, double *RATES, double *OLDRATES, double *STATES, double *OLDSTATES, double *ALGEBRAIC, double *CONDVAR)",
cleanCode(mDaeCodeInformation->rootInformationString()));
modelCode += functionCode("int computeDaeStateInformation(double *SI)",
cleanCode(mDaeCodeInformation->stateInformationString()));
modelCode += "\n";
modelCode += functionCode("int computeDaeVariables(double VOI, double *CONSTANTS, double *RATES, double *STATES, double *ALGEBRAIC, double *CONDVAR)",
cleanCode(genericCodeInformation->variablesString()));
}
// Check whether the model code contains a definite integral, otherwise
// compute it and check that everything went fine
if (modelCode.contains("defint(func")) {
mIssues << CellmlFileIssue(CellmlFileIssue::Error,
QObject::tr("definite integrals are not yet supported"));
} else if (!mCompilerEngine->compileCode(modelCode)) {
mIssues << CellmlFileIssue(CellmlFileIssue::Error,
mCompilerEngine->error());
}
// Keep track of the ODE/DAE functions, but only if no issues were reported
if (mIssues.count()) {
reset(true, false);
} else {
// Add the symbol of any required external function, if any
if (mAtLeastOneNlaSystem)
llvm::sys::DynamicLibrary::AddSymbol("doNonLinearSolve",
(void *) (intptr_t) doNonLinearSolve);
// Retrieve the ODE/DAE functions
mInitializeConstants = (InitializeConstantsFunction) (intptr_t) mCompilerEngine->getFunction("initializeConstants");
mComputeComputedConstants = (ComputeComputedConstantsFunction) (intptr_t) mCompilerEngine->getFunction("computeComputedConstants");
if (mModelType == CellmlFileRuntime::Ode) {
mComputeOdeRates = (ComputeOdeRatesFunction) (intptr_t) mCompilerEngine->getFunction("computeOdeRates");
mComputeOdeVariables = (ComputeOdeVariablesFunction) (intptr_t) mCompilerEngine->getFunction("computeOdeVariables");
} else {
mComputeDaeEssentialVariables = (ComputeDaeEssentialVariablesFunction) (intptr_t) mCompilerEngine->getFunction("computeDaeEssentialVariables");
mComputeDaeResiduals = (ComputeDaeResidualsFunction) (intptr_t) mCompilerEngine->getFunction("computeDaeResiduals");
mComputeDaeRootInformation = (ComputeDaeRootInformationFunction) (intptr_t) mCompilerEngine->getFunction("computeDaeRootInformation");
mComputeDaeStateInformation = (ComputeDaeStateInformationFunction) (intptr_t) mCompilerEngine->getFunction("computeDaeStateInformation");
mComputeDaeVariables = (ComputeDaeVariablesFunction) (intptr_t) mCompilerEngine->getFunction("computeDaeVariables");
}
// Make sure that we managed to retrieve all the ODE/DAE functions
bool functionsOk = mInitializeConstants
&& mComputeComputedConstants;
if (mModelType == CellmlFileRuntime::Ode) {
functionsOk = functionsOk
&& mComputeOdeRates
&& mComputeOdeVariables;
} else {
functionsOk = functionsOk
&& mComputeDaeEssentialVariables
&& mComputeDaeResiduals
&& mComputeDaeRootInformation
&& mComputeDaeStateInformation
&& mComputeDaeVariables;
}
if (!functionsOk) {
mIssues << CellmlFileIssue(CellmlFileIssue::Error,
QObject::tr("an unexpected problem occurred while trying to retrieve the model functions"));
reset(true, false);
}
}
}
ObjRef(const ObjRef<T>& aPtr)
{
mPtr = aPtr.getPointer();
if (mPtr != NULL)
mPtr->add_ref();
}
template<class T, class U> bool
operator!=(const ObjRef<T>& lhs, const ObjRef<U>& rhs)
{
return (lhs.getPointer() != rhs.getPointer());
}
QStringList CellmlFileRuntime::componentHierarchy(iface::cellml_api::CellMLElement *pElement)
{
// Make sure that we have a given element
if (!pElement)
return QStringList();
// Try to retrieve the component that owns the given element, unless the
// given element is a component itself (which will be the case when we come
// here through recursion)
ObjRef<iface::cellml_api::CellMLComponent> component = QueryInterface(pElement);
ObjRef<iface::cellml_api::CellMLElement> parent = pElement->parentElement();
ObjRef<iface::cellml_api::CellMLComponent> parentComponent = QueryInterface(parent);
if (!component && !parentComponent) {
// The element isn't a component and neither is its parent, so it
// doesn't have a hierarchy
return QStringList();
}
// Check whether this is an imported component and, if so, retrieve its
// imported name
QString componentName = QString::fromStdWString(component?component->name():parentComponent->name());
ObjRef<iface::cellml_api::CellMLElement> componentParent = component?component->parentElement():parentComponent->parentElement();
ObjRef<iface::cellml_api::CellMLElement> componentParentParent = componentParent->parentElement();
if (componentParentParent) {
// The given element comes from or is an imported component, so go
// through our different imported components and look for the one we are
// after
ObjRef<iface::cellml_api::CellMLImport> import = QueryInterface(componentParentParent);
ObjRef<iface::cellml_api::ImportComponentSet> importComponents = import->components();
ObjRef<iface::cellml_api::ImportComponentIterator> importComponentsIter = importComponents->iterateImportComponents();
for (ObjRef<iface::cellml_api::ImportComponent> importComponent = importComponentsIter->nextImportComponent();
importComponent; importComponent = importComponentsIter->nextImportComponent()) {
if (!componentName.compare(QString::fromStdWString(importComponent->componentRef()))) {
// This is the imported component we are after, so retrieve its
// imported name
componentName = QString::fromStdWString(importComponent->name());
break;
}
}
}
// Recursively retrieve the component hierarchy of the given element's
// encapsulation parent, if any
ObjRef<iface::cellml_api::CellMLComponent> componentEncapsulationParent = component?component->encapsulationParent():parentComponent->encapsulationParent();
return componentHierarchy(componentEncapsulationParent) << componentName;
}