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
MathMLTest::testCreateMathMLDocument()
{
iface::dom::DOMImplementation* di;
di = CreateDOMImplementation();
CPPUNIT_ASSERT(di);
CPPUNIT_ASSERT(di->hasFeature(L"org.w3c.dom.mathml", L"2.0"));
DECLARE_QUERY_INTERFACE_REPLACE(mdi, di, mathml_dom::MathMLDOMImplementation);
iface::mathml_dom::MathMLDocument* mdoc;
mdoc = mdi->createMathMLDocument();
CPPUNIT_ASSERT(mdoc);
// Get the document element...
iface::dom::Element* docel = mdoc->documentElement();
CPPUNIT_ASSERT(docel);
// Check it has the correct namespace URI and localName...
std::wstring nsURI = docel->namespaceURI();
std::wstring ln = docel->localName();
CPPUNIT_ASSERT_EQUAL(std::wstring(MATHML_NS), nsURI);
CPPUNIT_ASSERT_EQUAL(std::wstring(L"math"), ln);
// Check it has the correct type...
DECLARE_QUERY_INTERFACE(mel, docel, mathml_dom::MathMLElement);
CPPUNIT_ASSERT(mel);
mel->release_ref();
DECLARE_QUERY_INTERFACE(mmel, docel, mathml_dom::MathMLMathElement);
CPPUNIT_ASSERT(mmel);
mmel->release_ref();
docel->release_ref();
mdoc->release_ref();
mdi->release_ref();
}
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();
}
