END_TEST
START_TEST (test_comp_sbmldocument)
{
SBMLNamespaces sbmlns(3,1,"comp",1);
SBMLDocument doc(&sbmlns);
CompSBMLDocumentPlugin* docplugin = static_cast<CompSBMLDocumentPlugin*>(doc.getPlugin("comp"));
doc.setPackageRequired("comp", true);
fail_unless(docplugin->getRequired() == true);
fail_unless(docplugin->getNumModelDefinitions()==0);
ModelDefinition* moddef = docplugin->createModelDefinition();
moddef->setId("moddef1");
fail_unless(docplugin->getNumModelDefinitions()==1);
fail_unless(docplugin->addModelDefinition(NULL)==LIBSBML_INVALID_OBJECT);
ModelDefinition moddef2(3, 1);
moddef2.setId("moddef2");
fail_unless(docplugin->addModelDefinition(&moddef2)==LIBSBML_OPERATION_SUCCESS);
ModelDefinition* moddefref = docplugin->getModelDefinition("moddef2");
fail_unless(moddefref->getId()=="moddef2");
moddefref = docplugin->getModelDefinition(0);
fail_unless(moddefref->getId()=="moddef1");
moddef->setId("ID1");
fail_unless(moddefref->getId()=="ID1");
fail_unless(docplugin->removeModelDefinition(3)==NULL);
fail_unless(docplugin->removeModelDefinition(0)==moddef);
fail_unless(docplugin->getModelDefinition("moddef1")==NULL);
fail_unless(docplugin->getNumExternalModelDefinitions()==0);
ExternalModelDefinition* exmoddef = docplugin->createExternalModelDefinition();
exmoddef->setId("exmoddef1");
fail_unless(docplugin->getNumExternalModelDefinitions()==1);
fail_unless(docplugin->addExternalModelDefinition(NULL)==LIBSBML_INVALID_OBJECT);
ExternalModelDefinition exmoddef2(3, 1);
exmoddef2.setId("exmoddef2");
fail_unless(docplugin->addExternalModelDefinition(&exmoddef2)==LIBSBML_INVALID_OBJECT);
exmoddef2.setSource("where/the/file/is.xml");
fail_unless(docplugin->addExternalModelDefinition(&exmoddef2)==LIBSBML_OPERATION_SUCCESS);
ExternalModelDefinition* exmoddefref = docplugin->getExternalModelDefinition("exmoddef2");
fail_unless(exmoddefref->getId()=="exmoddef2");
exmoddefref = docplugin->getExternalModelDefinition(0);
fail_unless(exmoddefref->getId()=="exmoddef1");
exmoddef->setModelRef("ID1");
fail_unless(exmoddefref->getModelRef()=="ID1");
fail_unless(docplugin->removeExternalModelDefinition(3)==NULL);
fail_unless(docplugin->removeExternalModelDefinition(0)==exmoddef);
fail_unless(docplugin->getExternalModelDefinition("exmoddef1")==NULL);
}
// Gater all Symbols and setup SymbolRefs and referencedSymbols
void PharmML::setupSymbols() {
SymbolGathering gathering;
ModelDefinition *mdef = this->getModelDefinition();
// Gather all symbols
if (mdef->getParameterModel()) {
mdef->getParameterModel()->gatherSymbols(gathering);
}
mdef->getStructuralModel()->gatherSymbols(gathering);
for (VariabilityModel *vmod : mdef->getVariabilityModels()) {
vmod->gatherSymbols(gathering);
}
if (mdef->getCovariateModel()) {
mdef->getCovariateModel()->gatherSymbols(gathering);
}
for (auto const &om_model : mdef->getObservationModels()) {
om_model->gatherSymbols(gathering);
}
gathering.globalBlock();
if (this->independentVariable) {
gathering.addSymbol(this->independentVariable);
}
for (FunctionDefinition *fdef : this->getFunctionDefinitions()) {
gathering.addSymbol(fdef);
for (FunctionArgumentDefinition *farg : fdef->getArguments()) {
gathering.addSymbol(farg);
}
}
if (this->getTrialDesign()) { // Assume global namespace for DesignParameters
this->getTrialDesign()->gatherSymbols(gathering);
}
this->allSymbols = gathering.getAllSymbols();
gathering.setupAllSymbRefs();
// Handle referrers that are not symbols
this->setupRefererSymbRefs(gathering);
// Setup TargetMapping's (refers to Symbol's via strings)
this->setupTargetMappings(gathering);
}
void
CompIdBase::checkId (const ModelDefinition& x)
{
if (x.isSetId()) doCheckId(x.getId(), x);
}
LIBSBML_CPP_NAMESPACE_USE
int main(int argc,char** argv)
{
DynPkgNamespaces sbmlns;
sbmlns.addPackageNamespace("comp", 1, "comp");
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
document->setPackageRequired("dyn", true);
document->setPackageRequired("comp", true);
// create the Model
Model* model=document->createModel();
model->setId("grid2x2");
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("Loc1");
compartment->setConstant(false);
compartment->setSize(1);
compartment->setSpatialDimensions(2.0);
DynCompartmentPlugin* cplugin =
static_cast<DynCompartmentPlugin*>(compartment->getPlugin("dyn"));
SpatialComponent* component = cplugin->createSpatialComponent();
component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANX);
component->setVariable("q1_X");
component = cplugin->createSpatialComponent();
component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANY);
component->setVariable("q1_Y");
CompSBasePlugin* compPlugin =
static_cast<CompSBasePlugin*>(compartment->getPlugin("comp"));
ReplacedElement* relement = compPlugin->createReplacedElement();
relement->setIdRef("C");
relement->setSubmodelRef("GRID_1_1_cell");
compartment = model->createCompartment();
compartment->setId("Loc2");
compartment->setConstant(false);
compartment->setSize(1);
compartment->setSpatialDimensions(2.0);
cplugin =
static_cast<DynCompartmentPlugin*>(compartment->getPlugin("dyn"));
component = cplugin->createSpatialComponent();
component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANX);
component->setVariable("q2_X");
component = cplugin->createSpatialComponent();
component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANY);
component->setVariable("q2_Y");
compPlugin =
static_cast<CompSBasePlugin*>(compartment->getPlugin("comp"));
relement = compPlugin->createReplacedElement();
relement->setIdRef("C");
relement->setSubmodelRef("GRID_1_2_cell");
compartment = model->createCompartment();
compartment->setId("Loc3");
compartment->setConstant(false);
compartment->setSize(1);
compartment->setSpatialDimensions(2.0);
cplugin =
static_cast<DynCompartmentPlugin*>(compartment->getPlugin("dyn"));
component = cplugin->createSpatialComponent();
component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANX);
component->setVariable("q3_X");
component = cplugin->createSpatialComponent();
component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANY);
component->setVariable("q3_Y");
compPlugin =
static_cast<CompSBasePlugin*>(compartment->getPlugin("comp"));
relement = compPlugin->createReplacedElement();
relement->setIdRef("C");
relement->setSubmodelRef("GRID_2_1_cell");
compartment = model->createCompartment();
compartment->setId("Loc4");
compartment->setConstant(false);
compartment->setSize(1);
compartment->setSpatialDimensions(2.0);
cplugin =
static_cast<DynCompartmentPlugin*>(compartment->getPlugin("dyn"));
component = cplugin->createSpatialComponent();
component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANX);
component->setVariable("q4_X");
component = cplugin->createSpatialComponent();
component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANY);
component->setVariable("q4_Y");
compPlugin =
static_cast<CompSBasePlugin*>(compartment->getPlugin("comp"));
relement = compPlugin->createReplacedElement();
relement->setIdRef("C");
relement->setSubmodelRef("GRID_2_2_cell");
// create Parameters
Parameter* param = model->createParameter();
param->initDefaults();
param->setId("q1_X");
param->setValue(1);
param = model->createParameter();
param->initDefaults();
param->setId("q1_Y");
param->setValue(1);
param = model->createParameter();
param->initDefaults();
param->setId("q2_X");
param->setValue(2);
param = model->createParameter();
param->initDefaults();
param->setId("q2_Y");
param->setValue(1);
param = model->createParameter();
param->initDefaults();
param->setId("q3_X");
param->setValue(1);
param = model->createParameter();
param->initDefaults();
param->setId("q3_Y");
param->setValue(2);
param = model->createParameter();
param->initDefaults();
param->setId("q4_X");
param->setValue(2);
param = model->createParameter();
param->initDefaults();
param->setId("q4_Y");
param->setValue(2);
// create SubModels
CompModelPlugin* mplugin =
static_cast<CompModelPlugin*>(model->getPlugin("comp"));
Submodel* submodel = mplugin->createSubmodel();
submodel->setId("GRID_1_1_cell");
submodel->setModelRef("Cell");
submodel = mplugin->createSubmodel();
submodel->setId("GRID_1_2_cell");
submodel->setModelRef("Cell");
submodel = mplugin->createSubmodel();
submodel->setId("GRID_2_1_cell");
submodel->setModelRef("Cell");
submodel = mplugin->createSubmodel();
submodel->setId("GRID_2_2_cell");
submodel->setModelRef("Cell");
// create the ModelDefinition
CompSBMLDocumentPlugin* dplugin =
static_cast<CompSBMLDocumentPlugin*>(document->getPlugin("comp"));
ModelDefinition* mdef = dplugin->createModelDefinition();
mdef->setId("Cell");
compartment = mdef->createCompartment();
compartment->initDefaults();
compartment->setId("C");
compartment->setSpatialDimensions(2.0);
compartment->setSize(1.0);
Species* species = mdef->createSpecies();
species->setId("R");
species->setCompartment("C");
species->setHasOnlySubstanceUnits(false);
species->setBoundaryCondition(false);
species->setConstant(false);
species = mdef->createSpecies();
species->setId("S");
species->setCompartment("C");
species->setHasOnlySubstanceUnits(false);
species->setBoundaryCondition(false);
species->setConstant(false);
Reaction* reaction = mdef->createReaction();
reaction->setId("Degradation_R");
reaction->setReversible(false);
reaction->setFast(false);
reaction->setCompartment("C");
SpeciesReference* reactant = reaction->createReactant();
reactant->setSpecies("R");
reactant->setStoichiometry(1);
reactant->setConstant(true);
reaction = mdef->createReaction();
reaction->setId("Degradation_S");
reaction->setReversible(false);
reaction->setFast(false);
reaction->setCompartment("C");
reactant = reaction->createReactant();
reactant->setSpecies("S");
reactant->setStoichiometry(1);
reactant->setConstant(true);
document->checkConsistency();
Event* event = mdef->createEvent();
event->setId("event0");
event->setUseValuesFromTriggerTime(false);
DynEventPlugin* eplugin =
static_cast<DynEventPlugin*>(event->getPlugin("dyn"));
eplugin->setApplyToAll(true);
eplugin->setCboTerm("http://cbo.biocomplexity.indiana.edu/svn/cbo/trunk/CBO_1_0.owl#CellDivision");
Trigger* trigger = event->createTrigger();
trigger->setInitialValue(false);
trigger->setPersistent(false);
trigger->setMath(SBML_parseFormula("true"));
if (document->getNumErrors(LIBSBML_SEV_ERROR) > 0)
document->printErrors();
writeSBML(document,"dyn_example2.xml");
delete document;
}