void
AnnoToolsTest::setUp()
{
mATS = CreateAnnotationToolService();
if (mATS != NULL)
mAS = mATS->createAnnotationSet();
else
mAS = NULL;
}
void
doNameAnnotations(iface::cellml_api::Model* aModel,
iface::cellml_services::CodeGenerator* aCG)
{
// Make an annotation set...
iface::cellml_services::AnnotationToolService* ats
(CreateAnnotationToolService());
iface::cellml_services::AnnotationSet* as(ats->createAnnotationSet());
ats->release_ref();
aCG->useAnnoSet(as);
// Now we go through all variables in the model and set their annotations...
iface::cellml_api::CellMLComponentSet* ccs = aModel->allComponents();
iface::cellml_api::CellMLComponentIterator* cci = ccs->iterateComponents();
ccs->release_ref();
iface::cellml_api::CellMLComponent* comp;
while ((comp = cci->nextComponent()) != NULL)
{
iface::cellml_api::CellMLVariableSet* vs(comp->variables());
std::wstring compname = comp->name();
comp->release_ref();
iface::cellml_api::CellMLVariableIterator* vi(vs->iterateVariables());
vs->release_ref();
iface::cellml_api::CellMLVariable* v;
while ((v = vi->nextVariable()) != NULL)
{
std::wstring name = v->name();
std::wstring varn = compname;
varn += L"_";
varn += name;
std::wstring raten = L"rate_";
raten += varn;
as->setStringAnnotation(v, L"expression", varn.c_str());
as->setStringAnnotation(v, L"expression_d1", raten.c_str());
v->release_ref();
}
vi->release_ref();
}
cci->release_ref();
as->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);
}
}
}
jobject
Java_cellml_1bootstrap_AnnoToolsBootstrap_createAnnotationToolService(JNIEnv* env, jclass clazz)
{
RETURN_INTO_OBJREF(ats, iface::cellml_services::AnnotationToolService, CreateAnnotationToolService());
return wrap_cellml_services_AnnotationToolService(env, ats);
}
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();
}
int CellmlModelDefinition::instantiateCellmlApiObjects()
{
try
{
// create an annotation set to manage our variable usages
ObjRef<iface::cellml_services::AnnotationToolService> ats = CreateAnnotationToolService();
ObjRef<iface::cellml_services::AnnotationSet> as = ats->createAnnotationSet();
mCapi->annotations = as;
// mapping the connections between variables is a very expensive operation, so we want to
// only do it once and keep hold of the mapping (tracker item 3294)
ObjRef<iface::cellml_services::CeVASBootstrap> cvbs = CreateCeVASBootstrap();
ObjRef<iface::cellml_services::CeVAS> cevas = cvbs->createCeVASForModel(mCapi->model);
std::wstring msg = cevas->modelError();
if (msg != L"")
{
std::cerr << "loadModel: Error creating CellML Variable Association Service: "
<< ws2s(msg) << std::endl;
return -2;
}
mCapi->cevas = cevas;
// now check we can generate code and grab hold of the initial code information
ObjRef<iface::cellml_services::CodeGeneratorBootstrap> cgb = CreateCodeGeneratorBootstrap();
ObjRef<iface::cellml_services::CodeGenerator> cg = cgb->createCodeGenerator();
try
{
cg->useCeVAS(cevas);
ObjRef<iface::cellml_services::CodeInformation> cci = cg->generateCode(mCapi->model);
msg = cci->errorMessage();
if (msg != L"")
{
std::cerr << "CellmlModelDefintion::loadModel: Error generating code: "
<< ws2s(msg) << std::endl;
return -4;
}
// TODO: we are only interested in models we can work with?
if (cci->constraintLevel() != iface::cellml_services::CORRECTLY_CONSTRAINED)
{
std::cerr << "CellmlModelDefintion::loadModel: Model is not correctly constrained: "
<< std::endl;
return -5;
}
mCapi->codeInformation = cci;
// always flag all state variables and the variable of integration
ObjRef<iface::cellml_services::ComputationTargetIterator> cti = cci->iterateTargets();
while (true)
{
ObjRef<iface::cellml_services::ComputationTarget> ct = cti->nextComputationTarget();
if (ct == NULL) break;
if (ct->degree() > 0) break; // only want to initialise the base variables not the differential
ObjRef<iface::cellml_api::CellMLVariable> v(ct->variable());
if (ct->type() == iface::cellml_services::STATE_VARIABLE)
{
mVariableTypes[getVariableUniqueId(v)] = csim::StateType;
mVariableIndices[getVariableUniqueId(v)][csim::StateType] = mStateCounter;
mStateCounter++;
}
else if (ct->type() == iface::cellml_services::VARIABLE_OF_INTEGRATION)
{
mVariableTypes[getVariableUniqueId(v)] = csim::IndependentType;
mNumberOfIndependentVariables++;
}
else
{
// need to initialise the variable type
mVariableTypes[getVariableUniqueId(v)] = csim::UndefinedType;
}
}
}
catch (...)
{
std::cerr << "loadModel: Error generating the code information for the model" << std::endl;
return -3;
}
// if we get to here, everything worked.
mModelLoaded = true;
}
catch (...)
{
std::wcerr << L"Error instantiating CellML API objects." << std::endl;
return -1;
}
return csim::CSIM_OK;
}
