void
CUSESTest::setUp()
{
mCUSESBootstrap = CreateCUSESBootstrap();
mBootstrap = CreateCellMLBootstrap();
mModelLoader = mBootstrap->modelLoader();
}
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;
}
std::string getCellMLMetadataAsRDFXMLString(const char* mbrurl)
{
std::string s;
// Get the URL from which to load the model
if (!mbrurl) return(s);
std::wstring URL = string2wstring(mbrurl);
RETURN_INTO_OBJREF(cb, iface::cellml_api::CellMLBootstrap, CreateCellMLBootstrap());
RETURN_INTO_OBJREF(ml, iface::cellml_api::ModelLoader, cb->modelLoader());
// Try and load the CellML model from the URL
try
{
RETURN_INTO_OBJREF(model, iface::cellml_api::Model, ml->loadFromURL(URL.c_str()));
RETURN_INTO_OBJREF(rr, iface::cellml_api::RDFRepresentation,
model->getRDFRepresentation(L"http://www.cellml.org/RDFXML/string"));
if (rr)
{
DECLARE_QUERY_INTERFACE(rrs,rr,cellml_api::RDFXMLStringRepresentation);
std::wstring rdf = rrs->serialisedData();
s = wstring2string(rdf.c_str());
}
}
catch (...)
{
std::cerr << "getCellMLMetadataAsRDFXMLString: Error loading model URL: " << mbrurl << std::endl;
return(s);
}
return(s);
}
void
AnnoToolsTest::testStringAnnotation()
{
iface::cellml_api::CellMLBootstrap* bs = CreateCellMLBootstrap();
iface::cellml_api::DOMModelLoader* ml = bs->modelLoader();
bs->release_ref();
iface::cellml_api::Model* m =
ml->loadFromURL(BASE_DIRECTORY L"Ach_cascade_1995.xml");
CPPUNIT_ASSERT_NO_THROW(mAS->setStringAnnotation(m, L"thestring", L"hello"));
std::wstring anno = mAS->getStringAnnotation(m, L"thestring");
CPPUNIT_ASSERT_EQUAL(std::wstring(L"hello"), anno);
std::wstring anno2 = mAS->getStringAnnotationWithDefault(m, L"thestring", L"mystring");
CPPUNIT_ASSERT_EQUAL(std::wstring(L"hello"), anno2);
std::wstring anno3 = mAS->getStringAnnotationWithDefault(m, L"thestringno", L"mystring");
CPPUNIT_ASSERT_EQUAL(std::wstring(L"mystring"), anno3);
std::wstring fstr = mAS->prefixURI();
fstr += L"thestring";
iface::cellml_api::UserData* oa = m->getUserData(fstr.c_str());
CPPUNIT_ASSERT(oa);
oa->release_ref();
mAS->release_ref();
mAS = NULL;
CPPUNIT_ASSERT_THROW(oa = m->getUserData(fstr.c_str()), iface::cellml_api::CellMLException);
ml->release_ref();
m->release_ref();
}
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 main(int argc, char ** argv)
{
RETURN_INTO_OBJREF(cbs, iface::cellml_api::CellMLBootstrap,
CreateCellMLBootstrap());
RETURN_INTO_OBJREF(ml, iface::cellml_api::DOMModelLoader,
cbs->modelLoader());
try {
RETURN_INTO_OBJREF(model, iface::cellml_api::Model,
ml->loadFromURL(L"http://www.cellml.org/models/beeler_reuter_1977_version04/download"));
RETURN_INTO_WSTRING(cmid, model->cmetaId());
printf("Model's cmeta:id is %S\n", cmid.c_str());
} catch (iface::cellml_api::CellMLException& e) {
RETURN_INTO_WSTRING(msg, ml->lastErrorMessage());
printf("Got a CellML Exception loading a model. Error was %S\n",
msg.c_str());
return 1;
}
return 0;
}
void
CellMLEventsTest::setUp()
{
mGlycolysis = NULL;
mBootstrap = CreateCellMLBootstrap();
mModelLoader = mBootstrap->modelLoader();
mGlycolysis =
mModelLoader->loadFromURL
(BASE_DIRECTORY L"glycolysis_pathway_1997.xml");
QUERY_INTERFACE(mGlyET, mGlycolysis, events::EventTarget);
}
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;
}
void Tests::basicTests()
{
// Some very basic tests to make sure that we have access to the CellML API
// Get a bootstrap object and its model loader
ObjRef<iface::cellml_api::CellMLBootstrap> cellmlBootstrap = CreateCellMLBootstrap();
ObjRef<iface::cellml_api::DOMModelLoader> modelLoader = cellmlBootstrap->modelLoader();
QVERIFY(cellmlBootstrap);
QVERIFY(modelLoader);
// Create a CellML 1.0 model
ObjRef<iface::cellml_api::Model> cellml10Model = cellmlBootstrap->createModel(L"1.0");
QVERIFY(cellml10Model);
// Create a CellML 1.1 model
ObjRef<iface::cellml_api::Model> cellml11Model = cellmlBootstrap->createModel(L"1.1");
QVERIFY(cellml11Model);
// Create an invalid CellML model
ObjRef<iface::cellml_api::Model> invalidCellmlModel;
try {
invalidCellmlModel = cellmlBootstrap->createModel(L"xxx");
} catch (...) {
QVERIFY(!invalidCellmlModel);
}
// Load an existing model
ObjRef<iface::cellml_api::Model> existingModel = modelLoader->loadFromURL(QUrl::fromPercentEncoding(QUrl::fromLocalFile(QFileInfo(OpenCOR::fileName("models/noble_model_1962.cellml")).canonicalFilePath()).toEncoded()).toStdWString());
QVERIFY(existingModel);
QCOMPARE(QString::fromStdWString(existingModel->name()), QString("noble_model_1962"));
QCOMPARE(QString::fromStdWString(existingModel->cellmlVersion()), QString("1.0"));
// Load a non-existing model
ObjRef<iface::cellml_api::Model> nonExistingModel;
try {
nonExistingModel = modelLoader->loadFromURL(L"xxx");
} catch (...) {
QVERIFY(!nonExistingModel);
}
}
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
AnnoToolsTest::testObjectAnnotation()
{
iface::cellml_api::CellMLBootstrap* bs = CreateCellMLBootstrap();
iface::cellml_api::DOMModelLoader* ml = bs->modelLoader();
bs->release_ref();
iface::cellml_api::Model* m =
ml->loadFromURL(BASE_DIRECTORY L"Ach_cascade_1995.xml");
CPPUNIT_ASSERT_NO_THROW(mAS->setObjectAnnotation(m, L"theloader", ml));
iface::XPCOM::IObject* oa = mAS->getObjectAnnotation(m, L"theloader");
{
CPPUNIT_ASSERT(oa);
std::string o1 = oa->objid();
std::string o2 = ml->objid();
CPPUNIT_ASSERT(o1 == o2);
}
oa->release_ref();
oa = mAS->getObjectAnnotationWithDefault(m, L"theloader", NULL);
{
CPPUNIT_ASSERT(oa);
std::string o1 = oa->objid();
std::string o2 = ml->objid();
CPPUNIT_ASSERT(o1 == o2);
}
oa->release_ref();
oa = mAS->getObjectAnnotationWithDefault(m, L"theloaderno", NULL);
CPPUNIT_ASSERT(!oa);
std::wstring fstr = mAS->prefixURI();
fstr += L"theloader";
oa = m->getUserData(fstr.c_str());
CPPUNIT_ASSERT(oa);
oa->release_ref();
mAS->release_ref();
mAS = NULL;
CPPUNIT_ASSERT_THROW(oa = m->getUserData(fstr.c_str()), iface::cellml_api::CellMLException);
ml->release_ref();
m->release_ref();
}
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;
}
}
already_AddRefd<iface::cellml_services::DictionaryGenerator>
CDA_CeLEDSBootstrap::createDictGeneratorFromText(const std::wstring& XMLText)
throw(std::exception&)
{
mLoadError = L"";
RETURN_INTO_OBJREF(cb, iface::cellml_api::CellMLBootstrap,
CreateCellMLBootstrap());
RETURN_INTO_OBJREF(URLLoader, iface::cellml_api::DOMURLLoader,
cb->localURLLoader());
try
{
RETURN_INTO_OBJREF(langDoc, iface::dom::Document,
URLLoader->loadDocumentFromText(XMLText));
return new CDA_DictionaryGenerator(langDoc);
}
catch (...)
{
RETURN_INTO_WSTRING(lem, URLLoader->lastErrorMessage());
mLoadError = lem;
return NULL;
}
}
void
MaLaESTest::testMaLaESObject()
{
iface::cellml_services::MaLaESTransform* mt =
mMaLaESBootstrap->compileTransformer
(
L"opengroup: (\r\n"
L"closegroup: )\r\n"
L"abs: #prec[H]fabs(#expr1)\r\n"
L"and: #prec[20]#exprs[&&]\r\n"
L"arccos: #prec[H]acos(#expr1)\r\n"
L"arccosh: #prec[H]acosh(#expr1)\r\n"
L"arccot: #prec[1000(900)]atan(1.0/#expr1)\r\n"
L"arccoth: #prec[1000(900)]atanh(1.0/#expr1)\r\n"
L"arccsc: #prec[1000(900)]asin(1/#expr1)\r\n"
L"arccsch: #prec[1000(900)]asinh(1/#expr1)\r\n"
L"arcsec: #prec[1000(900)]acos(1/#expr1)\r\n"
L"arcsech: #prec[1000(900)]acosh(1/#expr1)\r\n"
L"arcsin: #prec[H]asin(#expr1)\r\n"
L"arcsinh: #prec[H]asinh(#expr1)\r\n"
L"arctan: #prec[H]atan(#expr1)\r\n"
L"arctanh: #prec[H]atanh(#expr1)\r\n"
L"ceiling: #prec[H]ceil(#expr1)\r\n"
L"cos: #prec[H]cos(#expr1)\r\n"
L"cosh: #prec[H]cosh(#expr1)\r\n"
L"cot: #prec[900(0)]1.0/tan(#expr1)\r\n"
L"coth: #prec[900(0)]1.0/tanh(#expr1)\r\n"
L"csc: #prec[900(0)]1.0/sin(#expr1)\r\n"
L"csch: #prec[900(0)]1.0/sinh(#expr1)\r\n"
L"diff: #lookupDiffVariable\r\n"
L"divide: #prec[900]#expr1/#expr2\r\n"
L"eq: #prec[30]#exprs[==]\r\n"
L"exp: #prec[H]exp(#expr1)\r\n"
L"factorial: #prec[H]factorial(#expr1)\r\n"
L"factorof: #prec[30(900)]#expr1 % #expr2 == 0\r\n"
L"floor: #prec[H]floor(#expr1)\r\n"
L"gcd: #prec[H]gcd_multi(#count, #exprs[, ])\r\n"
L"geq: #prec[30]#exprs[>=]\r\n"
L"gt: #prec[30]#exprs[>]\r\n"
L"implies: #prec[10(950)]!#expr1 || #expr2\r\n"
L"int: #prec[H]defint(func#unique1, BOUND, CONSTANTS, RATES, VARIABLES, #bvarIndex)#supplement double func#unique1(double* BOUND, double* CONSTANTS, double* RATES, double* VARIABLES) { return #expr1; }\r\n"
L"lcm: #prec[H]lcm_multi(#count, #exprs[, ])\r\n"
L"leq: #prec[30]#exprs[<=]\r\n"
L"ln: #prec[H]log(#expr1)\r\n"
L"log: #prec[H]arbitrary_log(#expr1, #logbase)\r\n"
L"lt: #prec[30]#exprs[<]\r\n"
L"max: #prec[H]multi_max(#count, #exprs[, ])\r\n"
L"min: #prec[H]multi_min(#count, #exprs[, ])\r\n"
L"minus: #prec[500]#expr1 - #expr2\r\n"
L"neq: #prec[30]#expr1 != #expr2\r\n"
L"not: #prec[950]!#expr1\r\n"
L"or: #prec[10]#exprs[||]\r\n"
L"plus: #prec[500]#exprs[+]\r\n"
L"power: #prec[H]pow(#expr1, #expr2)\r\n"
L"quotient: #prec[900(0)](int)(#expr1) / (int)(#expr2)\r\n"
L"rem: #prec[900(0)](int)(#expr1) % (int)(#expr2)\r\n"
L"root: #prec[1000(900)]pow(#expr1, 1.0 / #degree)\r\n"
L"sec: #prec[900(0)]1.0 / cos(#expr1)\r\n"
L"sech: #prec[900(0)]1.0 / cosh(#expr1)\r\n"
L"sin: #prec[H]sin(#expr1)\r\n"
L"sinh: #prec[H]sinh(#expr1)\r\n"
L"tan: #prec[H]tan(#expr1)\r\n"
L"tanh: #prec[H]tanh(#expr1)\r\n"
L"times: #prec[900]#exprs[*]\r\n"
L"unary_minus: #prec[950]-#expr1\r\n"
L"units_conversion: #prec[500(900)]#expr1*#expr2 + #expr3\r\n"
L"units_conversion_offset: #prec[500]#expr1+#expr2\r\n"
L"units_conversion_factor: #prec[900]#expr1*#expr2\r\n"
L"xor: #prec[25(30)](#expr1 != 0) ^ (#expr2 != 0)\r\n"
);
iface::cellml_api::CellMLBootstrap* cellbs = CreateCellMLBootstrap();
iface::cellml_api::DOMModelLoader* ml = cellbs->modelLoader();
cellbs->release_ref();
iface::cellml_api::Model* m = ml->loadFromURL
(BASE_DIRECTORY L"glycolysis_pathway_1997.xml");
ml->release_ref();
iface::cellml_services::CeVASBootstrap* cb =
CreateCeVASBootstrap();
iface::cellml_services::CeVAS* cev = cb->createCeVASForModel(m);
cb->release_ref();
iface::cellml_services::CUSESBootstrap* cub = CreateCUSESBootstrap();
iface::cellml_services::CUSES* cu =
cub->createCUSESForModel(m, false);
cub->release_ref();
iface::cellml_services::AnnotationToolService* ats =
CreateAnnotationToolService();
iface::cellml_services::AnnotationSet* as = ats->createAnnotationSet();
ats->release_ref();
iface::cellml_api::CellMLComponentSet* ccs = m->localComponents();
iface::cellml_api::CellMLComponent * glcC, * gts, * gp;
glcC = ccs->getComponent(L"Glc_C");
gts = ccs->getComponent(L"glucose_transport_system");
gp = ccs->getComponent(L"glucose_phosphorylation");
ccs->release_ref();
iface::cellml_api::CellMLVariableSet* vs = glcC->variables();
iface::cellml_api::CellMLVariable * vglcC, * vdelta_Glc_C_rxn1, * vdelta_Glc_C_rxn2;
vglcC = vs->getVariable(L"Glc_C");
vs->release_ref();
vs = gts->variables();
vdelta_Glc_C_rxn1 = vs->getVariable(L"delta_Glc_C_rxn1");
vs->release_ref();
vs = gp->variables();
vdelta_Glc_C_rxn2 = vs->getVariable(L"delta_Glc_C_rxn2");
vs->release_ref();
as->setStringAnnotation(vglcC, L"expression_d1",
L"first_derivative_of_glcC");
as->setStringAnnotation(vglcC, L"expression",
L"glcC");
as->setStringAnnotation(vdelta_Glc_C_rxn1, L"expression",
L"delta_Glc_C_rxn1");
as->setStringAnnotation(vdelta_Glc_C_rxn2, L"expression",
L"delta_Glc_C_rxn2");
iface::cellml_api::MathList* matl =
glcC->math();
iface::cellml_api::MathMLElementIterator* mei = matl->iterate();
iface::mathml_dom::MathMLElement* math = mei->next();
DECLARE_QUERY_INTERFACE(mmel, math, mathml_dom::MathMLMathElement);
math->release_ref();
mei->release_ref();
matl->release_ref();
iface::mathml_dom::MathMLElement* expr = mmel->getArgument(1);
mmel->release_ref();
iface::cellml_services::MaLaESResult* mr =
mt->transform(cev, cu, as, expr, glcC, NULL, NULL, 0);
CPPUNIT_ASSERT(mr);
std::wstring str = mr->compileErrors();
CPPUNIT_ASSERT_EQUAL(std::wstring(L""), str);
str = mr->expression();
CPPUNIT_ASSERT_EQUAL(std::wstring(L"first_derivative_of_glcC*0.00100000==1000.00*(1000.00*(delta_Glc_C_rxn1*0.00100000)+delta_Glc_C_rxn2)"), str);
uint32_t l = mr->supplementariesLength();
CPPUNIT_ASSERT_EQUAL(0, (int)l);
std::set<iface::cellml_api::CellMLVariable*> invVars;
iface::cellml_api::CellMLVariableIterator* cvi = mr->iterateInvolvedVariables();
iface::cellml_api::CellMLVariable* var;
while ((var = cvi->nextVariable()) != NULL)
{
CPPUNIT_ASSERT_EQUAL(0, (int)invVars.count(var));
invVars.insert(var);
}
cvi->release_ref();
std::set<iface::cellml_api::CellMLVariable*>::iterator invVarsI;
// Time is included in the count as well.
CPPUNIT_ASSERT_EQUAL(4, (int)invVars.size());
CPPUNIT_ASSERT_EQUAL(1, (int)invVars.count(vglcC));
CPPUNIT_ASSERT_EQUAL(1, (int)invVars.count(vdelta_Glc_C_rxn1));
CPPUNIT_ASSERT_EQUAL(1, (int)invVars.count(vdelta_Glc_C_rxn2));
for (invVarsI = invVars.begin(); invVarsI != invVars.end(); invVarsI++)
(*invVarsI)->release_ref();
cvi = mr->iterateBoundVariables();
var = cvi->nextVariable();
CPPUNIT_ASSERT(var != vglcC);
var->release_ref();
CPPUNIT_ASSERT(!cvi->nextVariable().getPointer());
cvi->release_ref();
CPPUNIT_ASSERT_EQUAL(1, (int)mr->getDiffDegree(vglcC));
CPPUNIT_ASSERT(!mr->involvesExternalCode());
mr->release_ref();
expr->release_ref();
vglcC->release_ref();
vdelta_Glc_C_rxn1->release_ref();
vdelta_Glc_C_rxn2->release_ref();
gts->release_ref();
gp->release_ref();
glcC->release_ref();
as->release_ref();
cu->release_ref();
cev->release_ref();
mt->release_ref();
m->release_ref();
}
CellMLModelDefinition::CellMLModelDefinition(const char* url) :
mURL(url)
{
//mCompileCommand = "gcc -fPIC -O3 -shared -x c -o";
mCompileCommand = "gcc -fPIC -g -shared -x c -o";
mTmpDirExists = false;
mCodeFileExists = false;
mDsoFileExists = false;
mSaveTempFiles = false;
mInstantiated = false;
nBound = -1;
nRates = -1;
nAlgebraic = -1;
nConstants = -1;
mNumberOfWantedVariables = 0;
mNumberOfKnownVariables = 0;
mNumberOfIndependentVariables = 0;
mStateCounter = 0;
mIntermediateCounter = 0;
mParameterCounter = 0;
mModel = NULL;
mCodeInformation = NULL;
mAnnotations = NULL;
std::cout << "Creating CellMLModelDefinition from the URL: "
<< url << std::endl;
if (! mURL.empty())
{
//std::cout << "Have a valid simulation description." << std::endl;
//std::cout << " CellML model URI: " << mURL.c_str() << std::endl;
RETURN_INTO_WSTRING(URL,string2wstring(mURL.c_str()));
RETURN_INTO_OBJREF(cb,iface::cellml_api::CellMLBootstrap,
CreateCellMLBootstrap());
RETURN_INTO_OBJREF(ml,iface::cellml_api::ModelLoader,cb->modelLoader());
iface::cellml_api::Model* model = (iface::cellml_api::Model*)NULL;
try
{
model = ml->loadFromURL(URL.c_str());
model->fullyInstantiateImports();
mModel = static_cast<void*>(model);
// create the annotation set
RETURN_INTO_OBJREF(ats,iface::cellml_services::AnnotationToolService,CreateAnnotationToolService());
iface::cellml_services::AnnotationSet* as = ats->createAnnotationSet();
mAnnotations = static_cast<void*>(as);
// make sure we can generate code and get the initial code information
RETURN_INTO_OBJREF(cgb,iface::cellml_services::CodeGeneratorBootstrap,
CreateCodeGeneratorBootstrap());
RETURN_INTO_OBJREF(cg,iface::cellml_services::CodeGenerator,
cgb->createCodeGenerator());
try
{
RETURN_INTO_OBJREF(cci,iface::cellml_services::CodeInformation,
cg->generateCode(model));
// need to keep a handle on the code information
cci->add_ref();
mCodeInformation = static_cast<void*>(cci);
// and add all state variables as wanted and the variable of integration as known
RETURN_INTO_OBJREF(cti,iface::cellml_services::ComputationTargetIterator,cci->iterateTargets());
while(1)
{
RETURN_INTO_OBJREF(ct,iface::cellml_services::ComputationTarget,cti->nextComputationTarget());
if (ct == NULL) break;
if (ct->type() == iface::cellml_services::STATE_VARIABLE)
{
as->setStringAnnotation(ct->variable(),L"flag",L"STATE");
as->setStringAnnotation(ct->variable(),L"array",L"OC_STATE");
as->setStringAnnotation(ct->variable(),L"array_index",formatNumber(mStateCounter).c_str());
mStateCounter++;
}
else if (ct->type() == iface::cellml_services::VARIABLE_OF_INTEGRATION)
{
as->setStringAnnotation(ct->variable(),L"flag",L"INDEPENDENT");
mNumberOfIndependentVariables++;
}
else if (ct->degree() > 0)
{
//as->setStringAnnotation(ct->variable(),L"flag-degree",L"WANTED");
//mNumberOfWantedVariables++;
}
}
}
catch (...)
{
std::wcerr << L"Error generating the code information for the model" << std::endl;
mCodeInformation = static_cast<void*>(NULL);
}
}
catch (...)
{
std::wcerr << L"Error loading model URL: " << URL.c_str() << std::endl;
mModel = static_cast<void*>(NULL);
}
}
}
int
main(int argc, char** argv)
{
// Get the URLs from which to load the model and the
// the language definition file
if (argc != 3)
{
printf("Usage: testCeLEDS modelURL languageDefinitionURL\n");
return -1;
}
wchar_t* modelURL;
size_t l = strlen(argv[1]);
modelURL = new wchar_t[l + 1];
memset(modelURL, 0, (l + 1) * sizeof(wchar_t));
const char* mbrurl = argv[1];
mbsrtowcs(modelURL, &mbrurl, l, NULL);
wchar_t* languageURL;
l = strlen(argv[2]);
languageURL = new wchar_t[l + 1];
memset(languageURL, 0, (l + 1) * sizeof(wchar_t));
const char* lbrurl = argv[2];
mbsrtowcs(languageURL, &lbrurl, l, NULL);
RETURN_INTO_OBJREF(cb, iface::cellml_api::CellMLBootstrap,
CreateCellMLBootstrap());
RETURN_INTO_OBJREF(ml, iface::cellml_api::ModelLoader,
cb->modelLoader());
ObjRef<iface::cellml_api::Model> mod;
try
{
mod = already_AddRefd<iface::cellml_api::Model>(ml->loadFromURL(modelURL));
if (mod == NULL)
throw L"";
}
catch (...)
{
printf("Error loading model URL.\n");
delete [] modelURL;
delete [] languageURL;
return -1;
}
delete [] modelURL;
RETURN_INTO_OBJREF(ceb, iface::cellml_services::CeLEDSExporterBootstrap,
CreateCeLEDSExporterBootstrap());
RETURN_INTO_OBJREF(ce, iface::cellml_services::CodeExporter,
ceb->createExporter(languageURL));
RETURN_INTO_WSTRING(le, ceb->loadError());
if (!le.empty()) {
wprintf(L"Could not load language definition file:\n");
wprintf(L" %ls\n",le.c_str());
return -1;
}
delete [] languageURL;
std::wstring code = ce->generateCode(mod);
wprintf(L"%ls", code.c_str());
return 0;
}
int
main(int argc, char** argv)
{
// Get the URL from which to load the model...
if (argc < 2)
{
printf("Usage: CellML2C modelURL\n");
return -1;
}
uint32_t usenames = 0, useida = 0;
for (int32_t i = 2; i < argc; i++)
{
if (!strcmp(argv[i], "usenames"))
usenames = 1;
else if (!strcmp(argv[i], "useida"))
useida = 1;
}
wchar_t* URL;
size_t l = strlen(argv[1]);
URL = new wchar_t[l + 1];
memset(URL, 0, (l + 1) * sizeof(wchar_t));
const char* mbrurl = argv[1];
mbsrtowcs(URL, &mbrurl, l, NULL);
iface::cellml_api::CellMLBootstrap* cb =
CreateCellMLBootstrap();
iface::cellml_api::ModelLoader* ml =
cb->modelLoader();
cb->release_ref();
iface::cellml_api::Model* mod;
try
{
mod = ml->loadFromURL(URL);
}
catch (...)
{
printf("Error loading model URL.\n");
// Well, a leak on exit wouldn't be so bad, but someone might reuse this
// code, so...
delete [] URL;
ml->release_ref();
return -1;
}
ml->release_ref();
delete [] URL;
mod->fullyInstantiateImports();
iface::cellml_services::CodeGeneratorBootstrap* cgb =
CreateCodeGeneratorBootstrap();
iface::cellml_services::CodeGenerator* cg;
iface::cellml_services::IDACodeGenerator* icg;
if (useida)
cg = icg = cgb->createIDACodeGenerator();
else
cg = cgb->createCodeGenerator();
cgb->release_ref();
if (usenames)
doNameAnnotations(mod, cg);
iface::cellml_services::CodeInformation* cci = NULL;
try
{
cci = cg->generateCode(mod);
}
catch (iface::cellml_api::CellMLException&)
{
printf("Caught a CellMLException while generating code.\n");
cg->release_ref();
mod->release_ref();
return -1;
}
catch (...)
{
printf("Unexpected exception calling generateCode!\n");
// this is a leak, but it should also never happen :)
return -1;
}
mod->release_ref();
cg->release_ref();
std::wstring m = cci->errorMessage();
if (m != L"")
{
printf("Error generating code: %S\n", m.c_str());
cci->release_ref();
return -1;
}
// We now have the code information...
WriteCode(cci, useida);
cci->release_ref();
return 0;
}
int
main(int argc, char** argv)
{
if (argc < 5)
{
printf("Usage: CustomGen modelURL wanted known unwanted\n"
"Each of wanted, known, and unwanted is a comma separated list.\n"
"Use a single comma to specify an empty list.\n"
"Each entry in the list should be in the form:\n"
" component/variable:degreeOfDerivative\n");
return -1;
}
std::wstring URL(MakeWideString(argv[1]));
std::set<std::pair<std::pair<std::wstring, std::wstring>, uint32_t> > wanted, known, unwanted;
TargetDescriptionToSet(argv[2], wanted);
TargetDescriptionToSet(argv[3], known);
TargetDescriptionToSet(argv[4], unwanted);
RETURN_INTO_OBJREF(cb, iface::cellml_api::CellMLBootstrap,
CreateCellMLBootstrap());
RETURN_INTO_OBJREF(ml, iface::cellml_api::ModelLoader,
cb->modelLoader());
// These assignments to NULL are only here in the test code to help look for
// memory errors by freeing things early... in production code, they wouldn't
// be necessary.
cb = NULL;
ObjRef<iface::cellml_api::Model> mod;
try
{
mod = already_AddRefd<iface::cellml_api::Model>(ml->loadFromURL(URL.c_str()));
}
catch (...)
{
printf("Error loading model URL.\n");
return -1;
}
RETURN_INTO_OBJREF(cgb, iface::cellml_services::CodeGeneratorBootstrap,
CreateCodeGeneratorBootstrap()
);
RETURN_INTO_OBJREF(cg, iface::cellml_services::CodeGenerator,
cgb->createCodeGenerator());
cgb = NULL;
cg->stateVariableNamePattern(L"VARS[%]");
RETURN_INTO_OBJREF(ccg, iface::cellml_services::CustomGenerator,
cg->createCustomGenerator(mod));
cg = NULL;
mod = NULL;
RETURN_INTO_OBJREF(cti, iface::cellml_services::ComputationTargetIterator,
ccg->iterateTargets());
while (true)
{
RETURN_INTO_OBJREF(ct, iface::cellml_services::ComputationTarget,
cti->nextComputationTarget());
if (ct == NULL)
break;
RETURN_INTO_OBJREF(cv, iface::cellml_api::CellMLVariable, ct->variable());
RETURN_INTO_WSTRING(compname, cv->componentName());
RETURN_INTO_WSTRING(varname, cv->name());
std::pair<std::pair<std::wstring, std::wstring>, uint32_t> p
(std::pair<std::wstring, std::wstring>(compname, varname), ct->degree());
if (wanted.count(p))
ccg->requestComputation(ct);
else if (known.count(p))
ccg->markAsKnown(ct);
else if (unwanted.count(p))
ccg->markAsUnwanted(ct);
}
cti = NULL;
RETURN_INTO_OBJREF(cci, iface::cellml_services::CustomCodeInformation,
ccg->generateCode());
ccg = NULL;
printf("Constraint level = ");
switch (cci->constraintLevel())
{
case iface::cellml_services::UNDERCONSTRAINED:
printf("UNDERCONSTRAINED\n");
break;
case iface::cellml_services::UNSUITABLY_CONSTRAINED:
printf("UNSUITABLY_CONSTRAINED\n");
break;
case iface::cellml_services::OVERCONSTRAINED:
printf("OVERCONSTRAINED\n");
break;
case iface::cellml_services::CORRECTLY_CONSTRAINED:
printf("CORRECTLY_CONSTRAINED\n");
break;
default:
printf("Unkown value\n");
}
printf("Index count: %u\n", cci->indexCount());
cti = already_AddRefd<iface::cellml_services::ComputationTargetIterator>(cci->iterateTargets());
while (true)
{
RETURN_INTO_OBJREF(ct, iface::cellml_services::ComputationTarget,
cti->nextComputationTarget());
if (ct == NULL)
break;
RETURN_INTO_OBJREF(cv, iface::cellml_api::CellMLVariable, ct->variable());
RETURN_INTO_WSTRING(compname, cv->componentName());
RETURN_INTO_WSTRING(varname, cv->name());
printf("* Computation target %S/%S:%u:\n", compname.c_str(), varname.c_str(),
ct->degree());
printf(" => Type = ");
switch (ct->type())
{
case iface::cellml_services::VARIABLE_OF_INTEGRATION:
printf("VARIABLE_OF_INTEGRATION - was marked as independent.\n");
break;
case iface::cellml_services::CONSTANT:
printf("CONSTANT - this should not happen!\n");
break;
case iface::cellml_services::STATE_VARIABLE:
printf("STATE_VARIABLE - was requested, and is available.\n");
break;
case iface::cellml_services::ALGEBRAIC:
printf("ALGEBRAIC - is used as an intermediate.\n");
break;
case iface::cellml_services::FLOATING:
printf("FLOATING - unused and not requested.\n");
break;
case iface::cellml_services::LOCALLY_BOUND:
printf("LOCALLY_BOUND - locally bound in expressions only.\n");
break;
case iface::cellml_services::PSEUDOSTATE_VARIABLE:
printf("PSEUDOSTATE_VARIABLE - target was requested, but could "
"not be computed from the independent variables and model.\n");
break;
default:
printf("Unknown type!\n");
}
RETURN_INTO_WSTRING(targname, ct->name());
printf(" => Name = %S\n", targname.c_str());
printf(" => Index = %u\n", ct->assignedIndex());
}
// To do: Print output from cci->iterateTargets();
RETURN_INTO_WSTRING(functionsString, cci->functionsString());
printf("Functions: %S\n", functionsString.c_str());
RETURN_INTO_WSTRING(code, cci->generatedCode());
printf("Code: %S\n", code.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
MathMLTest::setUp()
{
cb = CreateCellMLBootstrap();
}
int
main(int argc, char** argv)
{
// Fetch a bootstrap object. The bootstrap object is a special 'root' object
// from which you can get at everything else. CreateCellMLBootstrap() is a
// C++ binding specific method, which fetches the CellMLBootstrap object.
// It is the only non-OO method that you should ever call from the CellML
// API.
// ObjRef is a template defined in cellml-api-cxx-support.hpp. CreateCellMLBootstrap
// has already_Addrefd<iface::cellml_api::CellMLBootstrap> as its return type,
// which is the signal that a reference is added (i.e. the reference count is
// incremented on the return value, and the caller must ensure it is decremented).
// ObjRef will, when given an already_Addrefd argument, not increment the reference
// count, but will decrement it when it goes out of scope. If an ObjRef is constructed
// from a pointer or another ObjRef, it will add a reference on construction,
// and release the reference on destruction.
ObjRef<iface::cellml_api::CellMLBootstrap> cbs(CreateCellMLBootstrap());
// Now would be a good time to see what methods we can call. In the
// CellML_DOM_API source, find interfaces/CellML_APISPEC.idl.
// This defines the interfaces you can call. Search down to find
// this text...
/*
interface CellMLBootstrap
: XPCOM::IObject
{
...
*/
// We want to load a model, so we want the modelLoader attribute. We fetch
// the attribute like this...
ObjRef<iface::cellml_api::DOMModelLoader> ml(cbs->modelLoader());
// Suppose we only had a general model loader...
ObjRef<iface::cellml_api::ModelLoader> generalModelLoader(ml);
// if we wanted to get from this to a DOM model loader, we can't just cast,
// because the API is designed so it can work through bridges and we might
// need to switch to a different bridge (you can cast from an interface to a
// parent interface in the inheritance hierarchy, but not the other way).
// Instead, we call query_interface to ask the underlying object if it
// supports the interface we want, and to return us a value.
ObjRef<iface::cellml_api::DOMModelLoader> ml2(do_QueryInterface(generalModelLoader));
// ml2 would be null if generalModelLoader didn't support DOMModelLoader.
// Start a try, because we might get an exception...
try
{
// We now have a DOMModelLoader, stored in ml. DOMModelLoader inherits from
// ModelLoader, which defines a loadFromURL operation (check in the IDL).
// Be warned that is a synchronous (blocking) load. In a real application,
// you are probably better to download the file using another asynchronous
// http library, and then creating the model from the serialised text.
ObjRef<iface::cellml_api::Model> model(ml->loadFromURL(L"http://www.cellml.org/models/beeler_reuter_1977_version04/download"));
// Fetch the models cmeta:id (there obviously lots of other things we could
// do here!)
std::wstring cmid = model->cmetaId();
printf("Model's cmeta:id is %S\n", cmid.c_str());
}
// Most parts of the CellML API raise this exception. The DOM/MathML API, on the
// other hand, raises iface::dom::DOMException.
catch (iface::cellml_api::CellMLException&)
{
// Unfortunately, due to the need to support the 'lowest common
// denominator' of functionality in our bindings, exceptions can't have
// supplementary information (to suit XPCOM). However, many classes have
// a way to get the last error, e.g. lastErrorMessage on ModelLoader.
// However, threadsafety is potentially an issue with this.
std::wstring msg = ml->lastErrorMessage();
printf("Got a CellML Exception loading a model. Error was %S\n",
msg.c_str());
return 1;
}
return 0;
}
